JP7418470B2 - Integration of nucleic acid constructs into eukaryotic cells using transposase derived from Orydias - Google Patents

Description

Cross-reference of related applications

This application is filed in U.S. Provisional Application No. 62/831,092, filed on April 8, 2019, U.S. Provisional Application No. 62/873,338, filed on July 12, 2019, and No. 62/982,186, each of which is incorporated by reference in its entirety for all purposes.

Sequence listing reference

This application refers to the sequences disclosed in the txt file named 546916SEQLST.TXT of 2,254,295 bytes created on April 6, 2020, which is incorporated by reference.

2. Background Art The expression level of a gene encoded by a polynucleotide integrated into the genome of a cell depends on the configuration of sequence elements within the polynucleotide. Furthermore, the efficiency of introduction of polynucleotides, that is, the number of copies of polynucleotides introduced into each genome, and the position on the genome where introduction is performed also affect the expression level of genes encoded by polynucleotides. The efficiency with which a polynucleotide can be integrated into the genome of a target cell can often be increased by placing the polynucleotide in a transposon.

Transposons contain two ends that are recognized by transposases. Transposases act on transposons to remove them from one DNA molecule and incorporate them into another. The DNA between the two transposon ends is transferred together with the transposon ends by a transposase. The heterologous DNA sandwiched between a pair of transposon ends is recognized and transferred by a transposase, and is referred to herein as a synthetic transposon. When a synthetic transposon and its corresponding transposase are introduced into the nucleus of a eukaryotic cell, the transposon can be transferred into the cell's genome. Such results are useful because they can increase the efficiency of transformation and also increase the level of expression from the integrated heterologous DNA. Therefore, there is a need in the art for highly active transposases and transposons.

Transposition by transposases such as piggyBac is completely reversible. A transposon first integrates into an integrated target sequence within a recipient DNA molecule, during which duplication of the target sequence occurs at each end of the transposon's inverted terminal repeats (ITRs). The transposon is then removed by transposition, and the recipient DNA returns to its original sequence, with the duplicate target sequence and the transposon removed. However, this method is not sufficient to remove transposons from genomes in which they have integrated. Although the transposon is excised from the first integration target sequence, there is a high possibility that the transposon will integrate into the second integration target sequence in the genome. On the other hand, a transposase deficient in integration (or transposition) function will be able to excise the transposon from the first target sequence, but will not be able to integrate it into the second target sequence. Transposases lacking integration function are useful for reversing the integration of transposons into the genome.

One use of transposases is for the engineering of eukaryotic genomes. Such engineering may require the integration of one or more different polynucleotides into the genome. These incorporations may be simultaneous or sequential. Transfer of a first transposon containing a first heterologous polynucleotide into the genome by a first transposase is followed by transfer of a second transposon containing a second heterologous polynucleotide into the same genome by a second transposase. If carried out, it is advantageous that the second transposase does not recognize and introduce the first transposon. This is because the location of a polynucleotide sequence within the genome affects the expressivity of the gene encoded by that polynucleotide, so the transfer of the first transposon to a different chromosomal location by the second transposase This is because it may change the expression characteristics of any gene encoded by one heterologous polynucleotide. Therefore, there is a need for a set of transposons and their corresponding transposases, such that the transposase in the set recognizes and translocates only its corresponding transposon, but not other transposons in the set.

Since its discovery in 1983, the piggyBac transposon and transposase from the looper moth Trichoplusia ni has been widely used to insert foreign DNA into the genome of target cells from many different organisms. The piggyBac system is characterized by "activity in a wide range of organisms, the ability to integrate multiple large transgenes with high efficiency, the ability to add domains to transposases without loss of activity, and the ability to be excised from the genome without leaving footprint mutations" (Doherty et al. ., Hum. Gene Ther. 23, 311-320 (2012), at p. 312, LHC, ¶ 2), it is a particularly valuable transposase system.

The value and versatility of the piggyBac system has prompted significant efforts to identify other active piggyBac-like transposons (commonly referred to as piggyBac-like elements, or PLEs), but these have met with little success. "Since piggyBac is one of the most popular transposons used for transgenesis, the search for new active PLEs is attracting attention. However, only a few active PLEs have been reported to date." Luo et al., BMC Molecular Biology 15, 28 (2014) http://www.biomedcentral.com/1471-2199/15/28. p.4 of 12, RHC, ¶ 1 "Discussion").

Although there are many piggyBac transposon and transposase homologues in sequence databases, most are inactivated by the host to avoid harmful activity, as shown in the excerpt below. Few active ones have been identified. "Related piggyBac transposable elements have been found in plants, fungi, and animals, including humans [125], but they are likely inactivated by mutations." (Munoz-Lopez & Garcia-Perez, Current Genomics 11, 115-128 (2010) at p. 120, RHC, ¶ 1). "Transposons are thought to invade the genome during evolution and then spread throughout the genome. The 'selfish' mobility of transposons is detrimental to the host. Therefore, they are eliminated or inactivated by the host through natural selection. Even harmless transposons eventually lose their activity due to lack of conservative selection. As described above, transposons generally have a short lifespan within the host, and after that they become fossilized within the genome. (Hikosaka et al., Mol. Biol. Evol. 24, 2648-3656 (2007) at p. 2648, LHC, ¶ 1 "Introduction"). "The frequent movement of transposable elements within the genome is detrimental (Belancio et al., 2008; Deininger & Batzer, 1999; Le Rouzic & Capy, 2006; Oliver & Greene, 2009). As a result, most Transposable elements are inactivated shortly after entering a new host” (Luo et al., Insect Science 18, 652-662 (2011) at p. 660, LHC, ¶1).

Three classes of piggyBac-like elements have been found. (1) Very similar to the original piggyBac from Loopermoss (typically >95% identity at the nucleotide level). (2) moderately related (typically 30-50% identity at the amino acid level), and (3) very distantly related (Wu et al., Insect Science 15, 521 -528 (2008) at p. 521, RHC. ¶ 2).

PiggyBac-like transposases, which are highly related to the transposases of lupermoss, have been described by several groups. They are extremely well preserved. A transposase sequence very similar to the original piggyBac (95-98% nucleotide identity) has been reported in three different strains of the fruit fly Bactrocera dorsalis (Handler & McCombs, Insect Molecular Biology 9, 605- 612, (2000)). Relatively conserved piggyBac sequences have also been found in other Bactrocera species (Bonizzoni et al., Insect Molecular Biology 16, 645-650 (2007)). Additionally, in other strains of the two noctuid moths (Helicoverpa zea and Helicoverpa armigera) and the looper moth Trichoplusia ni, there are genomic copies of the piggyBac transposase with 93-100% nucleotide identity to the original piggyBac sequence. (Zimowska & Handler, Insect Biochemistry and Molecular Biology, 36, 421-428 (2006)). Zimowska & Handler also found multiple copies of a much more mutated (and truncated) version of the piggyBac transposase in both Helicoverpa species, as well as a homologue in the armworm Spodptera frugiperda. None of these groups attempted to measure the activity of these transposases. Wu et al. (2008) reported the isolation of a transposase from Macdunnoughia crassisigna with 99.5% sequence identity to looper moss piggyBac. They also showed that both resection and metastasis can be measured, indicating that this transposon and transposase are active. Their discussion summarizes the results as follows. “Other reported sequences of the closely related IFP2 class were in various Bactrocera species, the T. ni genome, Heliocoverpa armigera, and H. zea (Handler & McCombs, 2000; Zimowska & Handler, 2006; Bonizzoni et al. These sequences are partial fragments of piggyBac-like elements, many of which have been truncated or inactivated by the accumulation of random mutations.'' (Wu et. al., 2007). ., Insect Science 15, 521-528 (2008) at p. 526, LHC, ¶ 3.).

It turned out to be very difficult to identify an active piggyBac-like transposase that is moderately related to the enzyme in lupermoss by looking at the sequence alone. The presence of features known to be required (full-length open reading frame, catalytic aspartate residue, and intact ITRs) has not been shown to be predictive of activity. "The diversity of PLEs in eukaryotes has been revealed by computer analysis of genome sequence data (citation omitted). However, very few elements with intact structure consistent with function have been isolated. Only the original IFP2 piggyBac has been developed as a vector for routine transgenesis” (Wu et al., Genetica 139, 149-154 (2011), at p. 152, RHC, ¶ 2.). Wu et al.'s group at Nanjing University (hereinafter referred to as the "Nanjing group") published several papers over a six-year period, each identifying moderately related homologs of piggyBac. The Nanjing group showed in 2008 that it was possible to measure both excision and transposition of the Macdunnoughia crassisigna transposon by the corresponding transposase, and in subsequent papers they expressed a desire to identify piggyBac-like transposases with novel activities. , only one transposase from Aphis gossypii showed excision activity. They concluded that the utility of this transposase "needs to be investigated in future experiments" (Luo et. al. 2011, p. 660, LHC ¶ 2 "Discussion"). However, other papers published by the Nanjing group identified piggyBac-like sequences in various other insects, none of which showed any activity. Three papers have been published by a group at Kansas State University that identify other putatively active piggyBac-like transposases. None of these papers reported activity data. Wang et al. (Insect Molecular Biology 15, 435-443 (2006)) found multiple copies of piggyBac-like sequences in the genome of the tobacco budworm Heliothis virescens. Many of these had obvious mutations or deletions, and the authors did not consider them candidates for active transposases. In an article by Wang et al. (Insect Biochemistry and Molecular Biology 38, 490-498 (2008)), it was reported that more than 30 piggyBac-like sequences exist in the genome of the red flour beetle Tribolium castaneum. They stated, ``The TcPLEs identified here, with the exception of TcPLE1, are clearly defective due to the presence of multiple stop codons and/or indels in the transposase-encoding region.'' "There was no evidence to support a current mobilization event" (p. 492, section 3.1, ¶ ¶ 2&3). Wang et al. (2010) used PCR to identify a sequence similar to piggyBac from the pink bollworm Pectinophora gossypiella. Again, many apparently defective copies and one transposase with features that appeared to be active were found (page 179, RHC, ¶ 2). However, no follow-up reports showing transposase activity have been found. Other groups are also attempting to identify active piggyBac-like transposases. These reports conclude with a statement that the identified piggyBac-like elements are being tested for activity, but there are no follow-up reports of success. For example, Sarkar et al. (2003) conclude their Discussion by reiterating the value of a novel active piggyBac-like transposon and describing current efforts toward its identification. "The transfer of the original T. ni piggyBac element in various insects suggests that piggyBac family transposons may also be useful genetic tools in organisms other than insects. We have isolated an intact piggyBac element (AgaPB1) from which it was derived and tested its mobility in various organisms” (Mol. Gen. Genomics 270, 173-180 at p. 179, LHC, ¶1). There appear to be no further reports regarding this putatively active transposase. Xu et al. analyzed the silkworm genome and searched for piggyBac-like sequences (Xu et al., Mol Gen Genomics 276, 31-40 (2006)). They discovered 98 piggyBac-like sequences and performed various computer analyzes of putative transposase and ITR sequences. They conclude as follows. "We have isolated several intact piggyBac-like elements from B. mori and are currently testing their activity and potential use as transformation vectors" (p 38, RHC, ¶3). There appear to be no further published reports of these putatively active transposases.

There are four published papers discussing a distantly related third class of piggyBac-like transposases. These first three papers show only the ablated portion of the reaction and acknowledge that this is different from a complete metastasis. Hikosaka et al.'s paper (Mol Biol Evol 24, 2648-2656 (2007)) states, ``In this study, we showed that Xtr-Uribo2 Tpase has excision activity against target transposons, but the excised target "There is currently no evidence that it has been integrated into the genome" (p. 2654, RHC, ¶2). Luo et al. (Insect Science 18, 652-662 (2011)) said, ``These results demonstrate the activity of Ago-PLE1.1 transposase in mediating the first step of cut-and-paste movement of elements.'' reported (page 658, LHC, ¶1). The paper by Daimon et al. (Genome 53, 585-593 (2010)) discusses the transposase systems yabusabe-1 and yabusabe-W. Daimon et al. reported that they detected excision events by PCR, but even after screening approximately 100,000 recovered plasmids in which yabusame-1 and yabusame-W were excised, only a few recovered plasmids with excised elements remained. It is reported that none could be confirmed. On the other hand, Daimon reports the translocation frequency of the wild-type piggyBac enzyme to be approximately 0.3 to 1.4. Therefore, according to the report by Daimon et al., the frequency of excision of yabusabe-1 or -W appears to be less than 0.001% (1:100,000). This is at least 2-3 orders of magnitude lower than achieved with the wild-type piggyBac enzyme and even lower than genetically engineered piggyBac transposase variants that achieve 10-fold higher transposition than the wild type. Furthermore, the frequency of yabasume-1 translocation estimated by Daimon et al. is two orders of magnitude lower than the random integration frequency in mammalian cells (on the order of 0.1%). Thus, Daimon et al. show that yabusame-1 is essentially inactive and useless as a genetic manipulation tool. Such a view appears to underlie Daimon et al.'s own conclusion ("Although sensitive PCR-based assays were able to detect resection events, our data suggest that both elements almost completely suppress resection activity." (This shows that it has been lost.) Therefore, the PCR-based excision assays used to demonstrate the activity of Uribo2 and Ago-PLE1.1 are not predictive of metastatic activity, which is useful when inserting foreign DNA into the genome of target cells. It is suggested that there is no. The only report of a fully active piggyBac-like transposase (capable of both excision and integration), belonging to a third category distantly related to the piggyBac transposase from Trichoplusia Ni, is from the bat Myotis lucifugus. (Mitra et. al., Proc. Natl. Acad. Sci. 110, 234-239 (2013)). These authors demonstrated both excision and transposition activities of the bat transposase using a yeast system. All the studies presented here demonstrate that despite the large number of candidate sequences, identifying fully active piggyBac-like transposases is extremely difficult. Therefore, new piggyBac-like transposons and corresponding transposases are needed.

3. SUMMARY OF THE INVENTION Heterologous gene expression from polynucleotide constructs that stably integrate into the target cell genome is achieved by placing the expressed polynucleotide between a pair of transposon ends (sequence elements that are recognized and transferred by transposases). You can improve. A DNA sequence inserted between a pair of transposon ends is excised from the first DNA molecule by a transposase and inserted into a second DNA molecule. A novel piggyBac-like transposon-transposase system not derived from the looper moss Trichoplusia ni is disclosed. It is derived from the rice fish Oryzias latipes (Oryzias transposase and Oryzias transposon). Orydias transposons contain sequences that function as transposon ends, and in combination with the corresponding Orydias transposase that recognizes and acts on these transposon ends, can be used as a gene transfer system to stably introduce nucleic acids into cell DNA. Can be used. The gene transfer system of the present invention can be used in methods including, but not limited to, eukaryotic cell genome engineering, heterologous gene expression, gene therapy, cell therapy, insertional mutagenesis, or gene discovery.

Transposition may be performed using a polynucleotide comprising an open reading frame encoding an orydia transposase having an amino acid sequence at least 90% identical to SEQ ID NO: 782, operably linked to a heterologous promoter. A heterologous promoter may be active in eukaryotic cells. A heterologous promoter may be active in mammalian cells. mRNA may be prepared from a polynucleotide in which an open reading frame encoding an orydia transposase having an amino acid sequence at least 90% identical to SEQ ID NO: 782 is operably linked to a heterologous promoter that is active in an in vitro transcription reaction. good. The transposase may contain mutations shown in columns C and D of Table 1 with respect to the sequence of SEQ ID NO: 782. Transposase is 22, 124, 131, 138, 149, 156, 160, 164, 167, 171, 175, 177, 202, 206, 210, 214, 253, 258, 281 for the base sequence of SEQ ID NO: 782. , 284, 361, 386, 400, 408, 409, 455, 458, 467, 468, 514, 515, 524, 548, 549, 550, and 551. . The transposase is E22D, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, R175K, K177N, T202R, I206L, I210L, N214D, V253I, V258L, I 281F, The transposase has a mutation selected from A284L, L361I, V386I, M400L, S408E, L409I, F455Y, V458L, V467I, L468I, A514R, V515I, S524P, R548K, D549K, D550R, and S551R, and the transposase is selected from the above group. may optionally have at least 2, 3, 4, or 5. The amino acid sequence of the transposase can be selected from SEQ ID NO: 782 or 805-908. Transposases can excise or transpose transposons from SEQ ID NO:41. The excision or transposition activity of the transposase is at least 5% or 10% of the activity of SEQ ID NO: 782. The codons of the transposase open reading frame may be selected for expression in mammalian cells. The isolated mRNA may encode a polypeptide whose amino acid sequence is at least 90% identical to SEQ ID NO: 782, and the sequence of the mRNA at corresponding positions between the mRNA and SEQ ID NO: 781 is: Contains at least 10 synonymous codon differences to SEQ ID NO: 781, optionally with codons of the mRNA at corresponding positions selected for expression in mammalian cells. The open reading frame encoding the transposase may further encode a heterologous nuclear localization sequence fused to the transposase. The open reading frame encoding the transposase may further encode a heterologous DNA binding domain (eg, derived from the Crisper Cass system or zinc finger protein, or TALE protein) fused to the transposase. A non-naturally occurring polynucleotide may encode a polypeptide whose sequence is at least 90% identical to SEQ ID NO: 782.

The orydias transposon comprises SEQ ID NO: 7 and SEQ ID NO: 8 flanking heterologous polynucleotides. The transposon may further comprise a sequence at least 90% identical to SEQ ID NO: 12 on one side of the heterologous polynucleotide and a sequence at least 90% identical to SEQ ID NO: 15 on the other side. A heterologous polynucleotide may include a heterologous promoter that is active in eukaryotic cells. The promoter may be operably linked to at least one of the following: i) an open reading frame; ii) a nucleic acid encoding a selectable marker; iii) a nucleic acid encoding a counterselectable marker; iii) a nucleic acid encoding a regulatory protein; iv) a nucleic acid encoding an inhibitory RNA. A heterologous promoter may include a sequence selected from SEQ ID NOs: 325-409. A heterologous polynucleotide may include a heterologous enhancer that is active in eukaryotic cells. Heterologous enhancers may be selected from SEQ ID NOs: 304-324. Heterologous polynucleotides may include heterologous introns that can be spliced in eukaryotic cells. The nucleotide sequence of the heterologous intron may be selected from SEQ ID NOs: 412-472. The heterologous polynucleotide may include an insulator sequence. The insulator nucleic acid sequence may be selected from SEQ ID NOs: 286-292. A heterologous polynucleotide may include two open reading frames, each operably linked to a separate promoter. The heterologous polynucleotide may include a sequence selected from SEQ ID NOs: 596-779. The heterologous polynucleotide may include or encode a selectable marker. The selectable marker may be selected from glutamine synthetase, dihydrofolate reductase, puromycin acetyltransferase enzyme, blasticidin acetyltransferase enzyme, hygromycin B phosphotransferase enzyme, aminoglycoside 3'-phosphotransferase enzyme, and fluorescent protein. A eukaryotic cell having a genome comprising SEQ ID NO: 7 and SEQ ID NO: 8 flanking a heterologous polynucleotide is an embodiment of the invention. The cell may be an animal cell, a mammalian cell, a rodent cell or a human cell.

The transposon comprises (a) introducing a transposon containing SEQ ID NO: 7 and SEQ ID NO: 8 sandwiching a heterologous polynucleotide into the cell; (b) introducing into the cell a transposase having a sequence at least 90% identical to SEQ ID NO: 782; A transposase may be integrated into the genome of a eukaryotic cell by transposing the transposon to generate a genome comprising SEQ ID NO: 7 and SEQ ID NO: 8 flanking the heterologous polynucleotide. A transposase may be introduced as a polynucleotide encoding the transposase, and the polynucleotide may be an mRNA molecule or a DNA molecule. Furthermore, the transposase may be introduced as a protein. The heterologous polynucleotide may also encode a selectable marker, and the method may further include the step of selecting cells containing the selectable marker. The cells may be animal cells, mammalian cells, rodent cells, or human cells. The human cell may be a human immune cell, such as a B cell or a T cell. A heterologous polynucleotide may encode a chimeric antigen receptor. Polypeptides may be expressed from transposons integrated into the genome of eukaryotic cells. Polypeptides may be purified. Purified polypeptides may be incorporated into pharmaceutical compositions.

4. Brief description of the drawing
Structure of the Orydias transposon. Orydias transposons include a left transposon end and a right transposon end that flank a heterologous polynucleotide. The left transposon end contains (i) the left target sequence, which is often 5'-TTAA-3', although many other target sequences are used less frequently (Li et al., 2013. Proc. Natl Acad. Sci vol. 110, no. 6, E478-487). (ii) a left ITR (eg, SEQ ID NO: 7), and (iii) (optionally) an additional left transposon end sequence (eg, SEQ ID NO: 12). The right transposon end is (i) (optionally) an additional right transposon end sequence (e.g., SEQ ID NO: 15), (ii) a complete or incomplete repeat of the left ITR, but in an inverted orientation relative to the left ITR. (e.g., SEQ ID NO: 8), and (iii) a right target sequence that is typically the same as the left target sequence.

Detailed description of the invention

5. Detailed description of the invention
5.1 Definitions The use of the singular forms "a,""an," and "the" include plural references unless the context clearly dictates otherwise. Thus, for example, reference to "a polynucleotide" includes a plurality of polynucleotides, reference to "a substrate" includes a plurality of such substrates, reference to a "a variant" includes a plurality of such substrates, )” includes multiple variants.

Terms such as "connected," "attached," "coupled," and "coupled" are used herein interchangeably and unless the context clearly dictates otherwise. , including direct and indirect connections, attachments, connections, or couplings. When a range of values is stated, each intervening integer value and each fraction thereof between the upper and lower limits of the range must also be specifically disclosed, along with each subrange between such values. be understood. The upper and lower limits of any range can be independently included in or excluded from the range, and each range containing either, neither, or both limits is also contemplated by the invention. It is included. If the values being discussed have inherent limitations, for example if a component can exist in concentrations between 0 and 100%, or if the pH of an aqueous solution ranges from 1 to 14, those inherent limitations are clear. has been disclosed. It is understood that where a value is explicitly recited, values of the same amount or amounts as the recited value are also within the scope of the invention. Where combinations are disclosed, each subcombination of the elements of those combinations is also specifically disclosed and is within the scope of the invention. Conversely, when different elements or groups of elements are disclosed individually, combinations thereof are also disclosed. Also, where any element of the invention is disclosed as having multiple options, examples of the invention in which each option is excluded alone or in any combination with other options are also disclosed herein. be done. More than one element of the invention may have such an exclusion, and all combinations of elements with such an exclusion are disclosed herein.

Unless otherwise defined herein, all technical and scientific terms used herein are the same as commonly understood by one of ordinary skill in the art to which this invention belongs. have meaning. Singleton, et al., Dictionary of Microbiology and Molecular Biology, 2nd Ed., John Wiley and Sons, New York (1994), and Hale & Marham, The Harper Collins Dictionary of Biology, Harper Perennial, NY, 1991, It provides those skilled in the art with a general dictionary of many terms used in . Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. Unless otherwise specified, nucleic acids are written left to right in 5' to 3' orientation. Amino acid sequences are written from left to right, from amino to carboxy, respectively. Terms defined immediately below are more fully defined by reference to this entire specification.

"Configuration" of a polynucleotide refers to the functional sequence elements within the polynucleotide, as well as the order and orientation of those elements.

The terms "corresponding transposon" and "corresponding transposase" are used to indicate the active relationship between a transposase and a transposon. Transposase transposes the corresponding transposon. Many transposases may correspond to one transposon. A transposon is transposed by its corresponding transposase. Many transposons may correspond to a single transposase.

The term "counterselectable marker" refers to a polynucleotide sequence that confers a selective disadvantage on a host cell. Examples of counterselectable markers include sacB, rpsL, tetAR, pheS, thyA, gata-1, ccdB, kid, and barnase (Bernard, 1995, Journal/Gene, 162: 159-160; Bernard et al., 1994. Journal/Gene, 148: 71-74; Gababt et al., 1997, Journal/Biotechniques, 23: 938-941; Gababt et al., 1998, Journal/Gene, 207: 87-92; Gababt et al., 2000 , Journal/ Biotechniques, 28: 784-788; Galvao and de Lorenzo, 2005, Journal/Appl Environ Microbiol, 71: 883-892; Hartzog et al., 2005, Journal/Yeat, 22:789-798; Knipfer et al ., 1997, Journal/Plasmid, 37: 129-140; Reyrat et al., 1998, Journal/Infect Immun, 66: 4011-4017; Soderholm et al., 2001, Journal/Biotechniques, 31: 306-310, 312 Tamura et al., 2005, Journal/Appl Environ Microbiol, 71: 587-590; Yazynin et al., 1999, Journal/FEBS Lett, 452: 351-354). Counterselectable markers often confer a selective disadvantage in certain contexts. For example, it may confer susceptibility to a compound that can be added to the host cell's environment, or it may kill a host of one genotype but not a host of a different genotype. Conditions that do not impose a selective disadvantage on cells carrying a counterselectable marker are expressed as "permissive." Conditions that confer a selective disadvantage on cells with counterselectable markers are expressed as "restrictive."

The term "coupling element" or "translational coupling element" refers to a DNA sequence that makes it possible to link the expression of a first polypeptide to the expression of a second polypeptide. Internal ribosome entry site elements (IRES elements) and cis-acting hydrolase elements (CHYSEL elements) are examples of coupling elements.

The term "DNA sequence", "RNA sequence" or "polynucleotide sequence" refers to a contiguous nucleic acid sequence. This sequence can be anything from an oligonucleotide of 2-20 nucleotides in length to a full-length genomic sequence of thousands or hundreds of thousands of base pairs.

The term "expression construct" refers to any polynucleotide designed to transcribe RNA. For example, downstream genes, coding regions, polynucleotide sequences (e.g., cDNA or genomic DNA fragments encoding polypeptides or proteins, or RNA effector molecules, e.g., antisense RNA, triplex-forming RNA, ribozymes, artificially selected operably linked to an RNA molecule containing a double-stranded RNA, e.g., a stem-loop or hairpin dsRNA, or a bi-finger or multi-finger dsRNA, or a microRNA, or any RNA) A construct comprising at least one promoter that is or can be linked to a promoter. An "expression vector" is a polynucleotide that includes a promoter that can be operably linked to a second polynucleotide. Transfection or transformation of the expression construct into a recipient cell allows the cell to express the RNA effector molecule, polypeptide, or protein encoded by the expression construct. The expression construct may be a genetically engineered plasmid, virus, recombinant virus, or artificial chromosome derived from, for example, a bacteriophage, adenovirus, adeno-associated virus, retrovirus, lentivirus, poxvirus, herpesvirus, etc. Good too. Such expression vectors may contain sequences derived from bacteria, viruses, phage. Such vectors include vectors of chromosomal, episomal, viral origin, such as bacterial plasmids, bacteriophages, yeast episomes, yeast chromosomal elements, and viruses, vectors derived from combinations thereof, such as plasmids and Includes vectors derived from the genetic elements of bacteriophages, vectors derived from cosmids and phagemids, and the like. Expression constructs can be replicated in living cells or made synthetically. For the purposes of this application, the terms "expression construct," "expression vector," "vector," and "plasmid" are used interchangeably to indicate the application of the present invention in a general and exemplary sense. , it is not intended to limit the invention to a particular type of expression construct.

"Expressed polypeptide" means a polypeptide encoded by a gene on an expression construct.

The term "expression system" refers to any in vivo or in vitro biological system used to produce one or more gene products encoded by a polynucleotide.

"Gene" means a transcription unit that includes a promoter and the sequence from which it is to be expressed as RNA or protein. The sequence to be expressed may be genomic or cDNA, among other possibilities. Also, other elements such as introns and other control sequences may or may not be present.

A "gene transfer system" includes a vector or a gene transfer vector, or a polynucleotide containing a gene to be introduced cloned into a vector (a "gene transfer polynucleotide" or a "gene transfer construct"). The gene transfer system may also include other features to facilitate the process of gene transfer. For example, a gene transfer system may include a vector, a lipid or viral packaging mix to allow the first polynucleotide to enter the cell, a transposon, and productive genomic integration of the transposon. and a second polynucleotide sequence encoding a corresponding transposase for enhancing transposase. The transposase and transposon of the gene transfer system may be on the same or different nucleic acid molecules. Furthermore, the transposase of the gene introduction system may be provided as a polynucleotide or a polypeptide.

Two elements are "dissimilar" to each other if they are not naturally related. For example, a nucleic acid sequence encoding a protein linked to a heterologous promoter refers to a promoter other than the promoter that naturally drives expression of the protein. Heterologous nucleic acids flanked by transposon ends or ITRs refer to heterologous nucleic acids that are not naturally flanked by those transposon ends or ITRs and encode polypeptides other than transposases, including, for example, antibody heavy or light chains. Contains a nucleic acid that A nucleic acid is heterologous to a cell if it is not naturally present within the cell, or if it is naturally present within the cell but in a different location (eg, episomally or in a different genomic location).

The term "host" refers to any prokaryotic or eukaryotic organism that can be a recipient of a nucleic acid. As used herein, "host" includes prokaryotes or eukaryotes capable of genetic manipulation. For examples of such hosts, see Maniatis et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1982)). As used herein, the terms "host," "host cell," "host system," and "expression host" may be used interchangeably.

A "highly active" transposase is a transposase that is more active than the naturally occurring transposase from which it is derived. A "highly active" transposase is therefore not a naturally occurring sequence.

"Integration defective" or "transposition defective" refers to a transposase that is capable of excising the corresponding transposon but integrates the excised transposon into the host genome less frequently than the corresponding naturally occurring transposase.

"IRES" or "internal ribosome entry site" refers to a special sequence that directly facilitates ribosome binding independent of the cap structure.

An "isolated" polypeptide or polynucleotide refers to a polypeptide or polynucleotide that has been removed from its natural environment, produced using recombinant technology, or chemically or enzymatically synthesized. A polypeptide or polynucleotide of the invention may be purified, i.e., essentially free of other polypeptides or polynucleotides and associated cellular products or other impurities. good.

The terms "nucleoside" and "nucleotide" include those moieties that include the known purine and pyrimidine bases, as well as other modified heterocyclic bases. Such modifications include methylated purines or pyrimidines, acylated purines or pyrimidines, or other heterocycles. Modified nucleosides and nucleotides can also include modifications of the sugar moiety, for example, one or more hydroxyl groups are replaced with a halogen or aliphatic group, or functionalized with an ether or amine, etc. . The term "nucleotide unit" is intended to include nucleosides and nucleotides.

"Open reading frame" or "ORF" refers to the portion of a polynucleotide that, when translated into amino acids, does not contain a stop codon. The genetic code reads DNA sequences in groups of three base pairs, so a double-stranded DNA molecule can be read in one of six possible reading frames: three in the forward direction and three in the reverse direction. become. The ORF also contains a start codon for initiating translation.

The term "operably linked" refers to a functional linkage between two sequences such that one sequence modifies the behavior of the other sequence. For example, a first polynucleotide comprising a nucleic acid expression control sequence (such as a promoter, an IRES sequence, an enhancer, or an array of transcription factor binding sites) and a second polynucleotide may Operaably linked if it affects transcription and/or translation. Similarly, a first amino acid sequence and a second amino acid sequence that include a secretion signal or an intracellular localization signal may be used if the first amino acid sequence causes the second amino acid sequence to be secreted or localized within the cell; operably coupled.

The term "orthogonal" means that there is no interaction between the two systems. A first transposon and its corresponding first transposase, and a second transposon and its corresponding second transposase, are such that the first transposase does not excise or transpose the second transposon, and the second transposase does not excise or transpose the second transposon. If transposon 1 is not excised or transposed, it is orthogonal.

The term "overhang" or "DNA overhang" refers to a single-stranded portion at the end of a double-stranded DNA molecule. Complementary overhangs are those that base pair with each other.

"piggyBac-like transposase" means a transposase with at least 20% sequence identity to the piggyBac transposase from Trichoplusia ni (SEQ ID NO: 909), identified using the TBLASTN algorithm and described in Sakar, A. et. al. , (2003). Mol. Gen. Genomics 270: 173-180 (Molecular evolutionary analysis of the widespread piggyBac transposon family and related 'domesticated' species) and further characterized by a DDE-like DDD motif, with maximum alignment. In Trichoplusia ni piggyBac transposase, aspartic acid residues are present at positions corresponding to D268, D346, and D447. PiggyBac-like transposases are also characterized by their ability to excise transposons with high frequency and accuracy. A "piggyBac-like transposon" is a transposon that is identical or at least 80%, preferably at least 90, 95, 96, 97, 98 or 99% or 100% identical to the transposon end of a naturally occurring transposon encoding a piggyBac-like transposase. It means a transposon with an end. piggyBac-like transposons contain an inverted terminal repeat (ITR) sequence of about 12 to 16 bases at each end, and a 4-base sequence corresponding to the integration target sequence that is duplicated upon integration of the transposon (target site duplicate or target sequence duplicate or TSD) is sandwiched on both sides. PiggyBac-like transposons and transposases occur naturally in a wide range of organisms, including Argyrogramma agnate (GU477713), Anopheles gambiae (XP_312615; XP_320414; Agrotis ypsilon (GU477714), Bombyx mori (BAD11135), Ciona intestinalis (XP_002123602), Chilo suppressalis (JX294476), Drosophila melanogaster (AAL39784), Daphnia pulicaria (AAM76342), Helicoverpa armigera (ABS18391), Homo sapiens (NP_6 89808), Heliothis virescens ( ABD76335), Macdunnoughia crassisigna (EU287451), Macaca fascicularis (AB179012), Mus musculus (NP_741958), Pectinophora gossypiella (GU270322), Rattus norvegicus (XP_220453), Tribolium castaneum (XP_001814566) and Trichoplusia ni (AAA87375) and Xenopus tropicalis (BAF82026) However, metastatic activity has not been described for almost all of these.

The terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" are used interchangeably to refer to polymeric forms of nucleotides of any length, including ribonucleotides, deoxyribonucleotides, etc. or a mixture thereof. This term refers only to the primary structure of the molecule. Accordingly, this term includes triple-stranded, double-stranded and single-stranded deoxyribonucleic acid ("DNA"), as well as triple-stranded, double-stranded and single-stranded ribonucleic acid ("RNA"). Also included are forms modified, eg, by alkylation and/or capping, and unmodified forms of the polynucleotide. More specifically, the terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" include polydeoxyribonucleotides (including 2-deoxy-D-ribose), whether spliced or not; ), polyribonucleotides (containing D-ribose), including tRNA, rRNA, hRNA, siRNA and mRNA, other types of polynucleotides that are N- or C-glycosides of purine or pyrimidine bases, and non-nucleotide backbones Other polymers, such as polyamides (e.g., peptide nucleic acids (“PNAs”)) and polymorpholino (commercially available as Neugene from Anti-Virals, Inc., Corvallis, Oreg.) polymers, and other synthetic sequence-specific Nucleic acid polymers containing nucleobases in a configuration that allows for base pairing and base stacking as found in DNA and RNA. No difference in length is intended between the terms "polynucleotide," "oligonucleotide," "nucleic acid," and "nucleic acid molecule," and these terms are used interchangeably herein. has been done. These terms refer only to the primary structure of the molecule. Thus, these terms include, for example, 3'-deoxy-2', 5'-DNA, oligodeoxyribonucleotide N3' P5' phosphoramidates, 2'-O-alkyl substituted RNA, double-stranded and single-stranded Included are double-stranded DNA, as well as double-stranded and single-stranded RNA, and hybrids thereof, including, for example, hybrids between DNA and RNA, or hybrids between PNA and DNA or RNA, and also of known types. Modifications, such as labeling, alkylation, "capping", substitution of a nucleotide with one or more analogues, internucleotide modifications, such as those with uncharged linkages (e.g., methylphosphonates, phosphotriesters, phosphotriesters, roamidates, carbamates, etc.), those with negatively charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), and those with positively charged linkages (e.g., aminoalkyl phosphorolamines). proteins (including enzymes (e.g., nucleases), toxins, antibodies, signal peptides, poly-L-lysine, etc.); Some have intercalators (e.g., acridine, psoralen, etc.), some have chelates (e.g., of metals, radiometals, boron, oxidizing metals, etc.), some contain alkylating agents, some have modified linkages (e.g., α anomeric nucleic acids), and unmodified forms of polynucleotides or oligonucleotides.

"Promoter" means a nucleic acid sequence sufficient to direct transcription of an operably linked nucleic acid molecule. The promoter may be accompanied by or with other transcriptional control elements (e.g., enhancers) sufficient to enable promoter-dependent gene expression to be controlled in a cell type-specific, tissue-specific, or time-specific manner. It can be used without or can be induced by external signals or agents. Such elements may be within the 3' region of the gene or within introns. Desirably, the promoter is operably linked to a nucleic acid sequence, such as a cDNA or gene sequence, or an effector RNA coding sequence, in such a manner as to permit expression of the nucleic acid sequence, or the selection to be transcribed. A promoter is provided in an expression cassette into which the expressed nucleic acid sequence is conveniently inserted. A regulatory element such as a promoter that is active in mammalian cells refers to a regulatory element that is configured to achieve an expression level of at least one transcript per cell in mammalian cells into which the regulatory element has been introduced.

The term "selectable marker" refers to a polynucleotide segment or its expression product that allows, often under certain conditions, to select for or against a molecule or a cell containing it. The marker can encode an activity such as, but is not limited to, the production of RNA, peptides, or proteins, or provide a binding site for RNA, peptides, proteins, inorganic and organic compounds, or compositions. Examples of selectable markers include, but are not limited to, the following: (1) DNA segments that encode products that provide resistance to toxic compounds (e.g., antibiotics); (2) DNA segments that encode products that are lacking in recipient cells (e.g., tRNA genes, (3) DNA segments encoding products that suppress the activity of the gene product; (4) DNA segments encoding easily identifiable products (e.g., β-galactosidase, green fluorescent protein (GFP), ), phenotypic markers such as cell surface proteins), (5) DNA segments that bind to products that adversely affect cell survival or function, (6) DNA segments listed in Nos. 1 to 5 above. (7) a DNA segment that binds to a product that modifies the substrate (e.g., a restriction endonuclease); (8) isolates the desired molecule; (9) DNA segments that encode specific nucleotide sequences that may not be functional (e.g., for PCR amplification of subpopulations of molecules) , and/or (10) a DNA segment that, if absent, directly or indirectly confers sensitivity to a particular compound.

Sequence identity was determined using default gap parameters or by inspection using algorithms such as BESTFIT, FASTA, TFASTA, Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis. It can be determined by aligning the sequences and obtaining the best alignment (ie, yielding the highest percentage of sequence similarity over the comparison window). Percent sequence identity is calculated by comparing two optimally aligned sequences in a comparison window and determining the number of positions where the same residue appears in both sequences to find the number of matching positions. The percent sequence identity is calculated by dividing by the total number of matched and mismatched positions (ie, window size) without taking into account gaps in the comparison window, and multiplying the result by 100. Unless otherwise noted, the window for comparison between two sequences is defined over the length of the shorter of the two sequences.

A "target nucleic acid" is a nucleic acid into which a transposon is inserted. This target can be part of a chromosome, episome or vector.

An "integration target sequence" or "target sequence" or "target site" of a transposase is a site or sequence within a target DNA molecule into which a transposon can be inserted by a transposase. The piggyBac transposase from Trichoplusia ni inserts its transposon primarily into the target sequence 5'-TTAA-3'. Other available target sequences for piggyBac transposons are 5'-CTAA-3', 5'-TTAG-3', 5'-ATAA-3', 5'-TCAA-3', 5'-AGTT-3 ', 5'-ATTA-3', 5'-GTTA-3', 5'-TTGA-3', 5'-TTTA-3', 5'-TTAC-3', 5'-ACTA-3', 5'-AGGG-3', 5'-CTAG-3', 5'-GTAA-3', 5'-AGGT-3', 5'-ATCA-3', 5'-CTCC-3', 5' -TAAA-3', 5'-TCTC-3', 5'-TGAA-3', 5'-AAAT-3', 5'-AATC-3', 5'-ACAA-3', 5'-ACAT -3', 5'-ACTC-3', 5'-AGTG-3', 5'-ATAG-3', 5'-CAAA-3', 5'-CACA-3', 5'-CATA-3 ', 5'-CCAG-3', 5'-CCCA-3', 5'-CGTA-3', 5'-CTGA-3', 5'-GTCC-3', 5'-TAAG-3', 5'-TCTA-3', 5'-TGAG-3', 5'-TGTT-3', 5'-TTCA-3', 5'-TTCT-3', and 5'-TTTT-3' (Li et al., 2013. Proc. Natl. Acad. Sci vol. 110, no. 6, E478-487). PiggyBac-like transposases transpose transposons using a cut-and-paste mechanism in which a four-base pair target sequence is duplicated when inserted into a DNA molecule. In this way, target sequences are found on both sides of the integrated piggyBac-like transposon.

The term "translation" refers to the process by which a polypeptide is synthesized by ribosomes "reading" the sequence of a polynucleotide.

"Transposase" means a polypeptide that catalyzes the excision of a corresponding transposon from a donor polynucleotide, e.g., a vector, and (provided the transposase is not integration-defective) the subsequent integration of the transposon into a target nucleic acid. It is. "Orydias transposase" is a transposase having at least 80, 90, 95, 96, 97, 98, 99 or 100% sequence identity with SEQ ID NO: 782, including high activity variants of SEQ ID NO: 782, and corresponding It refers to a transposase that can transfer transposons. A highly active transposase is one that is more active in excision activity, transposition activity, or both than the naturally occurring transposase from which it is derived. A highly active transposase is preferably at least 1.5 times more active, or at least 2 times more active, or at least 5 times more active, or at least 10 times more active than the naturally occurring transposase from which it is derived, e.g. 2 to 5 times or 1.5 to 10 times. The transposase may or may not be fused to one or more additional domains, such as nuclear localization sequences or DNA binding proteins.

The term "transposition" as used herein refers to the action of a transposase that excises a transposon from one polynucleotide and then incorporates the transposon into a different site on the same polynucleotide or into a second polynucleotide. used to mean

The term "transposon" means a transposon that is excised from a first polynucleotide, e.g., a vector, and transferred to a second position in the same polynucleotide, e.g. refers to a polynucleotide that can be integrated into genomic DNA or extrachromosomal DNA. A transposon includes a first transposon end and a second transposon end, which are polynucleotide sequences that are recognized and transferred by a transposase. The transposon typically further comprises a first polynucleotide sequence between the two transposon ends, such that the first polynucleotide sequence is transposed together with the two transposon ends by the action of a transposase. This first polynucleotide of a natural transposon often contains an open reading frame encoding a corresponding transposase that recognizes and translocates the transposon. The transposons of the present invention are "synthetic transposons" that include a heterologous polynucleotide sequence that is juxtaposed between two transposon ends, thereby allowing transposition. Synthetic transposons may or may not further include flanking polynucleotide sequences outside the transposon ends, such as transposase-encoding sequences, vector sequences, or selectable marker-encoding sequences.

The term "transposon end" refers to a cis-acting nucleotide sequence sufficient for recognition and transposition by the corresponding transposase.
The transposon ends of piggyBac-like transposons contain complete or incomplete repeats such that each repeat in the two transposon ends is reverse complementary to each other. These are called inverted terminal repeats (ITR) or terminal inverted repeats (TIR). The transposon end may or may not contain additional sequences proximal to the ITR that promote or enhance transposition.

The term "vector" or "DNA vector" or "gene transfer vector" refers to a polynucleotide that is used to perform the "transport" function of another polynucleotide. For example, vectors are often used to propagate polynucleotides in living cells, to package polynucleotides for delivery into cells, or to integrate polynucleotides into the genomic DNA of cells. Vectors may also contain additional functional elements such as transposons.

5.2 Description
5.2.1 Genomic Integration Expression of genes from a heterologous polynucleotide in a eukaryotic host cell can be enhanced when the heterologous polynucleotide is integrated into the genome of the host cell. Additionally, by integrating polynucleotides into the host cell's genome, they are subjected to the same mechanisms that replicate and divide genomic DNA, making them generally stable and heritable. Such stable heritability is desirable to achieve good and stable expression over long growth periods. This is particularly important in cell therapy, where genetically modified cells are introduced into the body. It is also important for the production of biomolecules, particularly for therapeutic applications, where host stability and consistency of expression levels are also important for regulatory purposes. Therefore, cells that have integrated into their genome a gene transfer vector, including a transposon-based gene transfer vector, are an important embodiment of the present invention.

Heterologous polynucleotides may be more efficiently integrated into a target genome if they are part of a transposon (ie, placed between transposon ITRs), such as by a transposase. A particular advantage of transposons is that the entire polynucleotide between the transposon ITRs is integrated. A transposon containing a target site flanking ITRs flanking a heterologous polynucleotide integrates into the target site of the genome, resulting in a genome comprising a heterologous polynucleotide flanked by ITRs flanked by the target sites. This is in contrast to random integration, which typically occurs at a low frequency, where polynucleotides introduced into eukaryotic cells are often randomly fragmented within the cell, and only a portion of the polynucleotide is incorporated into the target genome. It is true. The piggyBac transposon from the piggyBac transposase revealed a functional nuclear targeting signal in the 94 C-terminal residues"). Heterologous polynucleotides integrated into piggyBac-like transposons may be integrated into eukaryotic cells, including animal cells, fungal cells, or plant cells. Preferred animal cells may be vertebrate or invertebrate. Preferred vertebrate cells include mammalian cells, including rodents such as rats, mice, hamsters, ungulates such as cows, goats, sheep, and pigs. Preferred vertebrate cells also include cells of human tissue and human stem cells. Target cells include hepatocytes, nervous system cells, muscle cells, blood cells, embryonic stem cells, somatic stem cells, hematopoietic cells, embryos, zygotes, sperm cells (some can be manipulated in vitro), and Includes immune cells including T cells, B cells, lymphocytes such as natural killer cells, T helper cells, antigen presenting cells, dendritic cells, neutrophils, and macrophages. Preferred cells are pluripotent cells (i.e. cells whose progeny can differentiate into some restricted cell type, such as hematopoietic stem cells or other stem cells) or totipotent cells (i.e. cells whose progeny can become any cell type of the organism). (e.g., embryonic stem cells). Preferred cultured cells are Chinese hamster ovary (CHO) cells or human embryonic kidney (HEK293) cells. Preferred fungal cells are yeast cells, including Saccharomyces cerevisiae and Pichia pastoris. Preferred plant cells are algae, such as chlorella, tobacco, corn, rice (Nishizawa-Yokoi et al (2014) Plant J. 77:454-63 "Precise marker excision system using an animal derived piggyBac transposon in plants") .

Preferred gene transfer systems include a transposon in combination with a corresponding transposase protein to transfer the transposon, or a nucleic acid encoding the corresponding transposase protein and capable of expression in the target cell. A preferred gene transfer system comprises a synthetic Orydias transposon and a corresponding Orydias transposase.

Transposase proteins may be present as proteins or as nucleic acids encoding transposases, e.g. as mRNA or ribonucleic acids containing polynucleotides recognized by the translational machinery of the cell, as DNA, e.g. as extrachromosomal DNA including episomal DNA, on plasmids, etc. It can be introduced into cells as DNA or as viral nucleic acids. Furthermore, nucleic acids encoding transposase proteins can be transfected into cells as nucleic acid vectors such as plasmids, or as gene expression vectors, including viral vectors. Transposase-encoding mRNA can be prepared using DNA in which the transposase-encoding gene is operably linked to a heterologous promoter, such as an in vitro active bacterial T7 promoter. DNA encoding a transposase protein can be stably inserted into the genome of a cell or into a vector for constitutive or inducible expression. When the transposase protein is transfected into cells or inserted into a vector as DNA, the transposase coding sequence is preferably operably linked to a heterologous promoter. There are various types of promoters, such as constitutive promoters, cell type-specific promoters, organism-specific promoters, tissue-specific promoters, and inducible promoters. When the DNA encoding the transposase is operably linked to a promoter and transfected into a target cell, it is desirable that the promoter be operable in the target cell. For example, if the target cell is a mammalian cell, the promoter should be operable in mammalian cells. If the target cell is a yeast cell, the promoter should be operable in yeast cells. If the target cell is an insect cell, the promoter should be operable in insect cells. If the cells of interest are human cells, the promoter should be operable in human cells. If the target cells are human immune cells, the promoter should be operable in human immune cells. All DNA or RNA sequences encoding piggyBac-like transposase proteins are expressly contemplated. Alternatively, the transposase may be directly introduced into cells as a protein (e.g., using cell-penetrating peptides (e.g., Ramsey and Flynn (2015) Pharmacol. Ther. 154: 78-86 "Cell-penetrating peptides therapeutic transports into cells"). cells"), using small molecules including salts and propanebetaine (e.g., Astolfo et al (2015) Cell 161: 674-690), or electroporation (e.g., Morgan and Day (1995)). Methods in Molecular Biology 48: 63-71 "The introduction of proteins into mammalian cells by electroporation").

Transposons can be inserted into a cell's DNA by non-homologous recombination through a variety of reproducible mechanisms, and can even be inserted in the absence of transposase activity. The transposons described herein can be used for gene transfer regardless of the gene transfer mechanism.

5.2.5 Gene Transfer Systems Gene transfer systems include polynucleotides that are introduced into host cells. Preferably, the polynucleotide comprises an orydias transposon and the polynucleotide integrates into the genome of the target cell.

Multiple components of the gene transfer system, e.g., one or more polynucleotides containing a gene for expression in the target cell, optionally including a transposon end, and a transposase (encoded by a nucleic acid, even if provided as a protein) (optional), these components can be transfected into cells simultaneously or sequentially. For example, a transposase protein or a nucleic acid encoding it can be transfected into a cell prior to, simultaneously with, or subsequent to transfection of the corresponding transposon. Furthermore, administration of any component of the gene transfer system may be repeated, eg, by administering this component at least twice.

Any of the transposase proteins described herein may be encoded by polynucleotides including RNA or DNA. Similarly, nucleic acids encoding transposase proteins or transposons of the invention can be transfected into cells as plasmids or as recombinant viral DNA, as linear or circular fragments.

Orydia transposase may be provided as a DNA molecule expressible in target cells. The sequence encoding the transposase should be operably linked to a heterologous sequence that enables expression of the transposase in the target cell. The sequence encoding the transposase may be operably linked to a heterologous promoter that is active in the target cell. For example, if the target cell is a mammalian cell, the promoter should be active in mammalian cells. If the target is a vertebrate cell, the promoter should be active in the vertebrate cell. If the cell of interest is a plant cell, the promoter should be active within the plant cell. If the promoter is in insect cells, the promoter should be active in insect cells. Additionally, the sequence encoding the transposase may be operably linked to other sequence elements necessary for expression in target cells, such as a polyadenylation sequence, a terminator sequence, etc.

The transposase may be provided as an mRNA expressible in target cells. mRNA is preferably prepared in an in vitro transcription reaction. For in vitro transcription, the orydias transposase encoding sequence is operably linked to a promoter that is active in the in vitro transcription reaction. For example, the T7 promoter (5'-TAATACGACTCACTATAG-3'), which allows transcription by T7 RNA polymerase, the T3 promoter (5'-AATTAACCCTCACTAAAG-3'), which allows transcription by T3 RNA polymerase, and the T3 promoter (5'-AATTAACCCTCACTAAAG-3'), which allows transcription by SP6 RNA polymerase. Contains the enabling SP6 promoter (5'-ATTTAGGTGACACTATAG-3'). Variants of these promoters, as well as other promoters that can be used for in vitro transcription, may also be operably linked to the orydias transposase encoding sequence.

When the transposase is provided as a polynucleotide (either DNA or mRNA) encoding the transposase, it is beneficial to improve the expression of the transposase in target cells. Therefore, it is advantageous to use sequences other than naturally occurring sequences to encode transposases, or in other words, to use the codon-preferences of the cell type in which expression is desired. For example, if the target cell is a mammalian cell, the codons should be biased towards the preferences found in mammalian cells. If the target is a vertebrate cell, the codons should be biased toward the preferences found in the particular vertebrate cell. If the target cell is a plant cell, the codons should be biased toward the preferences found in plant cells. If the promoter is an insect cell, the codons should be biased towards the preferences seen in insect cells.

Preferred RNA molecules include a suitable cap structure to facilitate translation in eukaryotic cells, polyadenylate and other 3' sequences to increase mRNA stability in eukaryotic cells, and reduce toxic effects on cells. including those having any substitutions to make it (for example, substitution of uridine with pseudouridine, and substitution of cytosine with 5-methylcytosine). The mRNA encoding the orydias transposase may be prepared with a 5' cap structure to improve expression in target cells. Exemplary cap structures include the cap analog (G(5')ppp(5')G), the anti-reverse cap analog (3'-O-Me-m ⁷ G(5')ppp(5')G) , clean cap (m7G(5')ppp(5')(2'OMeA)pG), and mCap (m7G(5')ppp(5')G). The mRNA encoding Orydia transposase may be prepared in which some bases are partially or completely substituted, for example, uridine is substituted with pseudo-uridine and cytosine is substituted with 5-methyl-cytosine. You can leave it there. Any combination of these caps and substitutions may be made.

Components of gene transfer systems include particle bombardment, electroporation, microinjection, combining components with lipid-containing vesicles such as cationic lipid vesicles, DNA condensation reagents (e.g., calcium phosphate, polylysine, polyethyleneimine), and One or more cells may be transfected by techniques such as inserting the nucleic acid component into a viral vector and contacting the viral vector with the cell. When a viral vector is used, the viral vector may be any of a variety of viral vectors known in the art, including viral vectors selected from the group comprising retroviral vectors, adenoviral vectors or adeno-associated viral vectors. may include. The gene transfer system may be formulated in any suitable manner as known in the art or as a pharmaceutical composition or kit.

5.2.3 Sequence elements in gene transfer systems Gene expression when a transgenic polynucleotide, such as a piggyBac-like transposon including an Orydias transposon, is integrated into the host cell genome is often strongly influenced by the chromatin environment in which the polynucleotide is integrated. be done. Polynucleotides that are integrated into euchromatin exhibit higher expression levels than polynucleotides that are integrated into heterochromatin or polynucleotides that are silenced after integration. Inclusion of chromatin control elements may reduce silencing of heterologous polynucleotides. It is therefore advantageous for the transgenic polynucleotide (including any of the transposons described herein) to contain chromatin control elements, such as sequences (insulators) that prevent heterochromatin spreading. Advantageous transgenic polynucleotides comprising transposons include an insulator sequence that is at least 95% identical to a sequence selected from one of SEQ ID NOs: 286-292; may include ubiquitously acting chromatin opening elements (UCOEs) or stabilizing and anti-repressor elements (STARs) to increase long-term stable expression from cells. Advantageous transgenic polynucleotides may further comprise a matrix attachment region, such as a sequence that is at least 95% identical to, for example, a sequence selected from one of SEQ ID NOs: 293-303.

In some cases, it is beneficial for the transgenic polynucleotide to contain two insulators, one on each side of the heterologous polynucleotide containing the sequence to be expressed, and within the transposon ITR. The insulators may be the same or different. Particularly advantageous transgenic polynucleotides have an insulator sequence that is at least 95% identical to a sequence selected from either SEQ ID NO: 291 or SEQ ID NO: 292, and a sequence selected from any of SEQ ID NOs: 286-290. and an insulator sequence that is at least 95% identical to. Insulators also shield expression control elements from each other. For example, if a transgenic polynucleotide contains a gene encoding two open reading frames, each operably linked to a different promoter, one promoter may reduce expression from the other, a phenomenon known as transcriptional interference. Sometimes I let it happen. Interposing an insulator sequence between the two transcription units that is at least 95% identical to a sequence selected from one of SEQ ID NOs: 286-292 reduces this interference and allows Expression can be increased.

Preferred gene transfer vectors contain expression elements capable of driving high levels of gene expression. In eukaryotic cells, gene expression is controlled by several different classes of elements, including enhancers, promoters, introns, RNA export elements, polyadenylation sequences, and transcription terminators.

Preferred gene transfer polynucleotides for the introduction of genes for expression into eukaryotic cells include an enhancer operably linked to the heterologous gene. Preferred gene transfer polynucleotides for the introduction of genes for expression into mammalian cells include the immediate early genes 1, 2 or 3 of cytomegalovirus (CMV) from either human, primate or rodent cells. (e.g., a sequence at least 95% identical to SEQ ID NO: 322), an enhancer from the adenovirus major late protein enhancer (e.g., a sequence at least 95% identical to SEQ ID NO: 323), or an enhancer from SV40 (e.g., a sequence at least 95% identical to SEQ ID NO: 323). (eg, a sequence at least 95% identical to SEQ ID NO: 324) and is operably linked to a heterologous gene.

Preferred gene transfer polynucleotides for the introduction of genes for expression into eukaryotic cells include a promoter operably linked to the heterologous gene. Advantageous transgenic polynucleotides for the introduction of genes for expression into mammalian cells include the EF1a promoter (e.g., SEQ ID NOS: 325-346) from any mammalian or avian species, including human, rat, mouse, chicken, and Chinese hamster. (e.g., any of SEQ ID NOs: 347-357) , a promoter of eukaryotic elongation factor 2 (EEF2) from any mammalian or avian species, including human, rat, mouse, chicken, Chinese hamster (e.g., any of SEQ ID NOs: 358-368), any mammal. or yeast GAPDH promoter (e.g., any of SEQ ID NO: 379-395), any mammalian or avian actin promoter (e.g., any of SEQ ID NO: 369-378), including human, rat, mouse, chicken, Chinese hamster. , a PGK promoter (e.g., any of SEQ ID NO: 396-402), or a ubiquitin promoter (e.g., SEQ ID NO: 403) from any mammalian or avian species, including human, rat, mouse, chicken, and Chinese hamster; operably linked to a gene. The promoter is operable by i) a heterologous open reading frame, ii) a nucleic acid encoding a selectable marker, iii) a nucleic acid encoding a counterselectable marker, iii) a nucleic acid encoding a regulatory protein, and iv) a nucleic acid encoding an inhibitory RNA. may be connected to.

Advantageous transgenic polynucleotides for gene transfer for expression in eukaryotic cells contain introns within the heterologous polynucleotide that can be spliced in the target cell. Gene transfer polynucleotides advantageous for gene transfer for expression in mammalian cells include the immediate early genes 1, 2 of cytomegalovirus (CMV) obtained from either human, primate, or rodent cells. 3 (e.g., a sequence at least 95% identical to any of SEQ ID NOs: 412-422), introns from mammalian or avian EF1a (e.g., SEQ ID NOs: 432-444) such as human, rat, mouse, chicken, Chinese hamster, etc. an intron from mammalian or avian EF2 (e.g., a sequence at least 95% identical to any of SEQ ID NOs: 464-471); an intron from actin of any mammalian or avian species, including human, rat, mouse, chicken, Chinese hamster (e.g., a sequence at least 95% identical to any of SEQ ID NOs: 445-458); human, rat, mouse, chicken; The GAPDH intron of any mammalian or avian species, including the Chinese hamster (e.g., a sequence at least 95% identical to any of SEQ ID NOs: 459-461), the intron containing the adenovirus major late protein enhancer (e.g., a sequence at least 95% identical to any of SEQ ID NOs: 462-463) or a hybrid/synthetic intron within a heterologous polynucleotide (eg, a sequence at least 95% identical to any of SEQ ID NOs: 423-431).

Preferred gene transfer polynucleotides for gene transfer for expression in eukaryotic cells include enhancers and promoters operably linked to a heterologous coding sequence. Such transgenic polynucleotides may contain an enhancer and promoter combination, in which an enhancer from one gene is combined with a promoter from a different gene, ie, the enhancer is heterologous to the promoter. For example, for gene introduction for expression in mammalian cells, the earliest CMV enhancer (such as a sequence selected from SEQ ID NOs: 304 to 322) derived from a rodent or human or primate is combined with a promoter from the EF1a gene (such as a sequence selected from SEQ ID NOs: 304 to 322). 325-346), or a promoter from a heterologous CMV gene (such as a sequence selected from SEQ ID NOs: 347-357), or a promoter from the EEF2 gene (sequences selected from SEQ ID NOs: 358-368). ), or a promoter from the actin gene (such as a sequence selected from SEQ ID NOs: 369-378), or a promoter from the GAPDH gene (such as a sequence selected from SEQ ID NOs: 379-395), advantageously followed by a heterologous sequence. Operaably connected.

Preferred gene transfer polynucleotides for gene transfer for expression in eukaryotic cells include a promoter and an intron operably linked to a heterologous open reading frame. Such gene transfer polynucleotides may include a combination of a promoter and an intron, in which the promoter of one gene is combined with an intron of a different gene, ie, the intron is heterologous to the promoter. For example, to introduce a gene for expression in mammalian cells, an intron from the EF1a gene ( an intron from the EEF2 gene (such as a sequence at least 95% identical to a sequence selected from SEQ ID NOs: 464-471); , or an intron from the actin gene, such as a sequence at least 95% identical to a sequence selected from SEQ ID NOs: 445-458, advantageously followed and operably linked to the heterologous sequence.

Advantageous transgenic polynucleotides for gene transfer for expression in eukaryotic cells contain a composite transcription initiation control element, including a promoter operably linked to an enhancer and/or an intron, and include a composite transcription initiation control element. The elements are operably linked in a heterogeneous array. Examples of advantageous composite transcription initiation control elements that can be operably linked to a heterologous sequence in a transgenic polynucleotide for gene transfer for expression in mammalian cells are sequences selected from SEQ ID NOs: 473-565. .

Expression of two open reading frames from a single polynucleotide can be achieved by operably linking the expression of each open reading frame to a separate promoter, each of which has an enhancer and Can be optionally operably linked to an intron. This is particularly useful when expressing two polypeptides that need to interact in a specific molar ratio, such as antibody chains or bispecific antibody chains, or a receptor and its ligand. For example, 3' of a polyadenylation sequence operably linked to a first open reading frame and 5' of a promoter operably linked to a second open reading frame encoding a second polypeptide; It is often beneficial to prevent transcriptional promoter interference by placing a genetic insulator between two open reading frames. Interference with transcriptional promoters can also be prevented by effectively terminating transcription of the first gene. In many eukaryotic cells, transcriptional interference can be reduced by using a strong polyA signal sequence between the two open reading frames. Examples of polyA signal sequences that can be used to effectively terminate transcription are given as SEQ ID NOs: 566-595. Preferred transgenic polynucleotides comprise a sequence at least 95% identical to a sequence selected from SEQ ID NOs: 566-595 operably linked to a heterologous open reading frame. Advantageous composite control elements for termination of transcription of a first gene and initiation of transcription of a second gene include the sequences given as SEQ ID NOs: 596-779. Particularly advantageous transgenic polynucleotides for the introduction of first and second open reading frames for co-expression in mammalian cells are at least 90% identical to sequences selected from SEQ ID NOs: 596-779; or at least 95% identical, or at least 99% identical, or 100% identical, separating two heterologous open reading frames.

5.2.4 Selection of target cells containing the transgenic polynucleotide If the transgenic polynucleotide contains an open reading frame encoding a selectable marker, the target cells are subjected to conditions that favor cells expressing the selectable marker (“selection conditions”). By exposure, target cells containing the introduced polynucleotide stably integrated into their genome can be identified. The transgenic polynucleotide may contain neomycin (resistance conferred by an aminoglycoside 3'-phosphotransferase (e.g., a sequence selected from SEQ ID NOs: 114-117)), puromycin (resistance conferred by a puromycin acetyltransferase (e.g., a sequence selected from SEQ ID NOs: 114-117)). Blasticidin (resistance conferred by blasticidin acetyltransferase and blasticidin deaminase (e.g., SEQ ID NO: 124)), hygromycin B (resistance conferred by hygromycin B phosphotransferase (sequence selected from conferring resistance to antibiotics such as zeocin (resistance conferred by a binding protein encoded by the ble gene (e.g. SEQ ID NO: 111)) It is advantageous to include open reading frames encoding selectable markers such as enzymes. Other selectable markers include those that fluoresce (such as open reading frames encoding GFP, RFP, etc.) and can therefore be selected using, for example, flow cytometry. Other selectable markers include open markers encoding transmembrane proteins that can bind to a second molecule (protein or small molecule) that can be fluorescently labeled, such that the presence of transmembrane proteins can be selected using flow cytometry, for example. Contains reading frame.

The transgenic polynucleotide may include a selectable marker open reading frame encoding glutamine synthetase (GS, eg, a sequence selected from SEQ ID NOs: 126-130) that allows selection via glutamine metabolism. Glutamine synthetase is an enzyme that biosynthesizes glutamine from glutamate and ammonia and is a key component of the unique pathway for glutamine formation in mammalian cells. In the absence of glutamine in the medium, GS enzymes are essential for the survival of mammalian cells in culture. Some cell lines, for example mouse myeloma cells, do not express enough GS enzyme to survive without the addition of glutamine. In such cells, the transfected GS open reading frame functions as a selectable marker by allowing growth in glutamine-free medium. Other cell lines, such as Chinese hamster ovary (CHO) cells, express sufficient GS enzyme to survive without exogenous addition of glutamine. These cell lines can use genome editing techniques such as CRISPR/CAS9 to reduce or eliminate the activity of the GS enzyme. In either of these cases, GS inhibitors such as methionine sulfoximine (MSX) can be used to inhibit the endogenous GS activity of the cell. The selection protocol involves introducing a transgenic polynucleotide comprising a first polypeptide and a sequence encoding a glutamine synthase selectable marker, followed by treating the cells with an inhibitor of glutamine synthetase, such as methionine sulfoximine. . The higher the level of methionine sulfoximine used, the higher the level of glutamine synthetase expression necessary to enable the cells to synthesize enough glutamine to survive. Some of these cells will also exhibit increased expression of the first polypeptide.

Preferably, the GS open reading frame is operably linked to a weak promoter or other sequence element that attenuates expression, as described herein, so that many copies of the transgenic polynucleotide are present. High-level expression is only possible if the protein is integrated into the genome at a location where high-level expression occurs. In such cases, it may not be necessary to use the inhibitor methionine sulfoximine, and if glutamine synthetase expression is attenuated, it may be sufficient to synthesize enough glutamine for cell survival. It may become possible to make tough choices.

The transgenic polynucleotide contains dihydrofolate reductase (DHFR, e.g., SEQ ID NO: 112-113)). Some cell lines do not express enough DHFR to survive without the addition of hypoxanthine and thymidine (HT). In such cells, the transfected DHFR open reading frame functions as a selectable marker by allowing growth in media lacking hypoxanthine and thymidine. DHFR-deficient cell lines (eg, Chinese hamster ovary (CHO) cells) can be created by reducing or eliminating the activity of the endogenous DHRF enzyme using genome editing techniques such as CRISPR/CAS9. DHFR confers resistance to methotrexate (MTX). DHFR can be inhibited by higher levels of methotrexate. The selection protocol involves introducing a construct containing a sequence encoding a first polypeptide and a DHFR selectable marker into cells with or without a functional endogenous DHFR gene, followed by inhibition of DHFR, such as methotrexate. including treating the cells with an agent. The higher the level of methotrexate used, the higher the level of DHFR expression necessary for the cells to synthesize enough DHFR to survive. Also, some of these cells show increased expression of the first polypeptide. Preferably, the DHFR open reading frame is such that high level expression can only occur if many copies of the transgenic polynucleotide are present or integrated at a location in the genome where high level expression occurs. , a weak promoter or other sequence element that attenuates expression as described above.

High-level expression is encoded by a transgenic polynucleotide that is integrated into a region of the genome that is highly transcriptionally active, integrated into the genome in multiple copies, or located extrachromosomally in multiple copies. can be obtained from genes that have been operably linking the open reading frame encoding the selectable marker to an expression control element such that expression of the selectable polypeptide from the transgenic polynucleotide is low and/or using conditions that provide more stringent selection; It is often beneficial to do so. Under these conditions, the transgenic polynucleotide must be expressed at high levels within the genome of the cell in order for the expressing cell to produce sufficient levels of the selectable polypeptide encoded by the transgenic polynucleotide to survive the selection conditions. or a sufficiently high copy number of the transgenic polynucleotide can be present such that these factors compensate for the low level of expression achievable due to the expression control elements.

Genomic integration of a transposon in which a selectable marker is operably linked to a regulatory element that only weakly expresses the marker typically requires insertion of the transposon into the target genome by a transposase (e.g., Section 6.1). (see .3). By operably linking a selectable marker to a weakly expressed element, cells are selected that have integrated multiple copies of the transposon or have integrated the transposon at a genomic location suitable for high expression. By using a gene transfer system containing a transposon and its corresponding transposase, there is a high possibility of obtaining cells in which multiple copies of the transposon have been integrated, or cells in which the transposon has been integrated at a genomic location suitable for high expression. . Gene transfer systems comprising a transposon and its corresponding transposase are therefore particularly advantageous when the transposon comprises a selectable marker operably linked to a weak promoter.

The nucleic acid and selectable marker expressed as RNA or protein are contained on the same transgenic polynucleotide, but may be operably linked to different promoters. In this case, a phosphoglycerokinase (PGK) promoter (e.g. a promoter selected from SEQ ID NO: 396-402), a herpes simplex virus thymidine kinase (HSV-TK) promoter (e.g. SEQ ID NO: 405), a MC1 promoter (e.g. Low expression levels of selectable markers can be achieved by using constitutive promoters with weak activity, such as the ubiquitin promoter (eg, SEQ ID NO: 403). Other weakly active promoters can be intentionally constructed, such as promoters attenuated by truncations, such as the truncated SV40 promoter (e.g., sequences selected from SEQ ID NOs: 407-408), the truncated HSV- TK promoter (e.g., SEQ ID NO: 404), or promoters attenuated by inserting a 5'UTR unfavorable to expression between the promoter and the open reading frame encoding the selectable polypeptide (e.g., SEQ ID NO: 410 to 411). Particularly advantageous transgenic polynucleotides include a promoter sequence selected from SEQ ID NO: 396-409 operably linked to an open reading frame encoding a selectable marker.

Also, the expression level of the selectable marker can be advantageously reduced by other mechanisms such as inserting the SV40 small t antigen intron after the selectable marker open reading frame. The SV40 small t antigen intron accepts an aberrant 5' splice site, which results in deletions within the preceding open reading frame in some spliced mRNAs, thereby reducing selectable marker expression. obtain. A particularly advantageous transgenic polynucleotide comprises an intron SEQ ID NO: 472 operably linked to an open reading frame encoding a selectable marker. For this attenuation mechanism to be effective, the open reading frame encoding the selectable marker preferably contains a strong intron donor within its coding region. DNA sequences SEQ ID NOs: 131-134 are exemplary nucleic acid sequences encoding glutamine synthetase sequences having SEQ ID NOs: 126-129, respectively. Each of these nucleic acid sequences contains an intron donor and can be operably linked to the SV40 small t antigen intron by placing the intron in the 3'UTR of the glutamine synthetase open reading frame. SEQ ID NO: 123 is an exemplary nucleic acid sequence encoding puromycin acetyltransferase SEQ ID NO: 122, which sequence includes an intron donor and, by placing this intron in the 3'UTR of the puromycin open reading frame, It may be operably linked to the SV40 small t antigen intron. Advantageous gene transfer polynucleotides are at least 90% identical, or at least 95% identical, or at least Contains 99% identical or 100% identical sequences.

Also, the expression level of a selectable marker can be advantageously reduced by other mechanisms, such as, for example, inserting an inhibitory 5'-UTR into a transcript such as SEQ ID NOs: 410-411. Particularly advantageous transgenic polynucleotides include a promoter operably linked to an open reading frame encoding a selectable marker, wherein the promoter is at least 90% identical, or at least 95% identical, or at least A sequence that is 99% identical or 100% identical is interposed between the promoter and the selectable marker.

Exemplary nucleic acid sequences comprising a glutamine synthetase coding sequence operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 152-221 and 283-285. A transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 152-221 or 283-285, when integrated into the genome of a target cell, expresses glutamine synthetase, thereby causing the cell to react in the absence of added glutamine. Helps grow under or in the presence of MSX. The regulatory elements of these sequences are balanced to ensure low levels of glutamine synthetase expression, and target cells with genomes containing multiple copies of the transgenic polynucleotide or genomes that favor expression of the encoding gene. It provides a selective advantage to target cells whose genome has a region copied with the transgenic polynucleotide. Preferred transgenic polynucleotides include sequences selected from SEQ ID NOs: 152-221 or 283-285, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising a blasticidin-S-transferase coding sequence operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 222-228. A transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 222-228, when integrated into the genome of a target cell, expresses blasticidin-S-transferase, thereby causing the cell to detect the presence of added blasticidin. Helps grow underneath. The regulatory elements of these sequences are balanced to ensure low levels of expression of blasticidin-S-transferase, and target cells with genomes containing multiple copies of the transgenic polynucleotide and expression of the encoding gene. This provides a selective advantage to target cells whose genomes have been copied with the gene-transfer polynucleotide in genomic regions that are advantageous for this purpose. Advantageous transgenic polynucleotides include sequences selected from SEQ ID NOs: 222-228, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising a hygromycin B phosphotransferase coding sequence operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 229-230. Once integrated into the genome of the target cell, the transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 229-230 expresses hygromycin B phosphotransferase, thereby allowing the cell to grow in the presence of added hygromycin. help you do. The control elements of these sequences are balanced to result in low levels of hygromycin B phosphotransferase expression, and target cells whose genomes are composed of multiple copies of the transgenic polynucleotide, as well as expression of the encoding gene. Copies of the transgenic polynucleotide are organized in genomic regions that are advantageous to the target cell, resulting in a selective advantage over the target cell. Advantageous transgenic polynucleotides include sequences selected from SEQ ID NOs: 229-230, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising aminoglycoside 3'-phosphotransferase coding sequences operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 221-223 and 259-260. A transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 221-223 and 259-260, when integrated into the genome of a target cell, expresses aminoglycoside 3'-phosphotransferase, thereby causing the cell to respond to added neomycin. Helps you grow in your presence. The control elements of these sequences are balanced to result in low levels of aminoglycoside 3'-phosphotransferase expression and are useful in target cells whose genomes consist of multiple copies of the transgenic polynucleotide or in the encoding gene. Provides a selective advantage to target cells that contain a copy of the transgenic polynucleotide in a genomic region favorable for expression. Preferred transgenic polynucleotides include sequences selected from SEQ ID NOs: 221-223 and 259-260, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising puromycin acetyltransferase coding sequences operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 234-253 and 261-285. A transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 234-253 or 261-285, when integrated into the genome of a target cell, expresses puromycin acetyltransferase, thereby causing the cell to respond to the presence of added puromycin. Helps grow underneath. The regulatory elements of these sequences are balanced to produce low levels of expression of puromycin acetyltransferase, and target cells with genomes with multiple copies of the transgenic polynucleotide or genomic regions that favor expression of the encoding gene. provides a selective advantage over target cells whose genomes have been copied with the transgenic polynucleotide. Advantageous transgenic polynucleotides include sequences selected from SEQ ID NOs: 234-253 or 261-285, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising a ble gene coding sequence operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 254-258. The transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 254-258, when integrated into the genome of the target cell, expresses the ble gene, thereby helping the cell to grow in the presence of added zeocin. . The regulatory elements of these sequences are balanced to yield low levels of ble gene product expression, favoring expression of the encoding gene in target cells whose genomes are composed of multiple copies of the transgenic polynucleotide. This provides a selective advantage to target cells in which copies of the transgenic polynucleotide are present in specific genomic regions. Advantageous transgenic polynucleotides include sequences selected from SEQ ID NOs: 254-258, which may further include a left transposon end and a right transposon end.

Exemplary nucleic acid sequences comprising a dihydrofolate reductase coding sequence operably linked to control sequences expressible in mammalian cells include SEQ ID NOs: 135-151 and 259-282. A transgenic polynucleotide comprising a sequence selected from SEQ ID NOs: 135-151 or 259-282, when integrated into the genome of a target cell, expresses dihydrofolate reductase, thereby causing the cell to absorb added hypoxanthine and Helps grow in the absence of thymidine or in the presence of MTX. The control elements of these sequences are balanced to result in low levels of dihydrofolate reductase expression, and are useful in target cells whose genomes consist of multiple copies of the transgenic polynucleotide or in genomes that favor expression of the encoding gene. It has a selective advantage over target cells consisting of a copy of the transgenic polynucleotide in the region. Advantageous transgenic polynucleotides include sequences selected from SEQ ID NOs: 135-151 or 259-282, which may further include a left transposon end and a right transposon end.

The use of transposons and transposases in combination with weakly expressed selectable markers has several advantages over non-transposon constructs. One is that in the case of transposons, there is a good linkage between the expression of the first polypeptide and the selectable marker, since the transposase integrates the entire sequence between the two transposon ends into the genome. be. On the other hand, when foreign DNA is introduced into the nucleus of a eukaryotic cell, such as a mammalian cell, it is gradually broken down into random fragments that are either integrated into the cell's genome or degraded. Therefore, if a transgenic polynucleotide containing a sequence encoding a first polypeptide and a selectable marker is introduced into a cell population, some cells will incorporate the sequence encoding the selectable marker, but some cells will not incorporate the sequence encoding the first polypeptide. Sequences that are included may not be included, or vice versa. Therefore, selection of cells that express a large amount of the selectable marker has only a slight correlation with cells that also express a large amount of the first polypeptide. In contrast, since the transposase incorporates all sequences between the transposon ends, cells that express high levels of the selectable marker are likely to also express high levels of the first polypeptide.

A second advantage of transposons and transposases is that they are much more efficient for integrating DNA sequences into the genome. Therefore, a much higher proportion of the cell population is likely to integrate one or more copies of the transgenic polynucleotide into their genome, and thus both the selectable marker and the first polypeptide are well stabilized. The probability of occurrence increases accordingly.

A third advantage of piggyBac-like transposons and transposases is that piggyBac-like transposases are biased toward inserting their corresponding transposons into transcriptionally active chromatin. Therefore, each cell is likely to integrate the transgenic polynucleotide into a region of the genome where the gene is well expressed and, accordingly, both the selectable marker and the first polypeptide are likely to be stably expressed. Become.

5.2.5 Novel piggyBac-like transposase from ORYZIAS LATIPES Natural DNA transposons undergo a "cut-and-paste" fashion of replication, where the transposon is excised from a first DNA molecule and inserted into a second DNA molecule. DNA transposons are characterized by ITRs (inverted terminal repeats) and are recruited by transposases encoded by the elements. The piggyBac transposon/transposase system is particularly useful because it allows for precise transposon integration and excision (see, e.g., "Fraser, MJ (2001) The TTAA-Specific Family of Transposable Elements: Identification, Functional Characterization, and Utility for Transformation of Insects. Insect Transgenesis: Methods and Applications. AM Handler and AA James. Boca Raton, Fla., CRC Press: 249-268"; and "US 20070204356 A1: PiggyBac constructs in vertebrates" and references therein).

Although many sequences with sequence similarity to the piggyBac transposase from Trichoplusia ni have been found in the genomes of phylogenetically different species from fungi to mammals, none have been shown to have transposase activity. Very few (see, for example, Wu M, et al (2011) Genetica 139 :149-54. "Cloning and characterization of piggyBac-like elements in lepidopteran insects" and references therein).

Two properties of transposases of particular interest for genome modification are the ability to integrate polynucleotides into the target genome and the ability to precisely excise polynucleotides from the target genome. Any of these properties can be measured using an appropriate system.

A system for measuring the first step of transposition, excision of the transposon from the first polynucleotide, includes the following components: A transposon comprising (i) a first polynucleotide encoding a first selectable marker operably linked to a sequence to be expressed in a selected host, and (ii) a transposon end that is recognized by a transposase. The transposon is present within the first selectable marker and interrupts the coding sequence of the first selectable marker such that the first selectable marker is not activated. The transposon is placed at the first selectable marker such that precise excision of the first transposon reconstitutes the first selectable marker. When an active transposase capable of excising the first transposon is introduced into a host cell containing the first polynucleotide, the host cell expresses an active first selectable marker. The activity of the transposase to excise the transposon can be measured as the frequency with which the host cell is allowed to proliferate under conditions requiring the first selectable marker to be active.

If the transposon contains a second selectable marker operably linked to a sequence that enables expression of the second selectable marker in a selected host, transfer of the second selectable marker into the genome of the host cell results in an active A genome containing the first and second selectable markers is obtained. The activity of the transposase in introducing the transposon into the second genomic location can be measured as the frequency with which the host cell is able to proliferate under conditions that require the first and second selectable markers to be active. . On the other hand, if the first selectable marker is present and the second selectable marker is absent, then the transposon was excised from the first polynucleotide, but the transposon was not subsequently introduced into the second polynucleotide. It is thought that this indicates that The selectable marker may be, for example, an open reading frame encoding an antibiotic resistance protein, or an auxotrophic marker, or any other selectable marker.

We used such a system to test the activity of putative transposase/transposon combinations as described in section 6.1. Using computational methods, they searched publicly sequenced genomes for open reading frames with homology to known active piggyBac-like transposases. We selected a transposase sequence that appeared to have a DDDE motif characteristic of active piggyBac-like transposases and searched the DNA sequences flanking this putative transposase for inverted repeat sequences flanking the 5'-TTAA-3' target sequence. . As a result, Spodoptera litura (Genebank Accession No. MTZO01002002.1, Protein Accession Pieris rapae (NCBI genome reference number NW_ 019093607.1, GeneBank Protein Accession Myzus persicae (NCBI genome reference number NW_019100532.1), which has an open reading frame encoding the putative transposase of SEQ ID NO. session number XP_022166603), Onthophagus taurus (NCBI genome reference number NW_019280463, protein accession number ), Temnothorax curvispinosus (NCBI Genome Reference Number NW_020220783.1, Protein Accession Number , Agrlius planipenn (NCBI Genome Reference No. NW_020442437.1, Protein Accession No. Parasteatoda tepidariorum (NCBI Genome Reference Number NW_018371884.1, Protein Accession Number Pectinophora gossypiella (GeneBank Accession No. GU270322.1, Protein ID ADB45159.1, Wang et al. al, 2010. Insect Mol. Biol. 19, 177-184. Also described in "piggyBac-like elements in the pink bollworm, Pectinophora gossypiella"), sandwiched between the putative left end of SEQ ID NO: 84 and the putative right end of SEQ ID NO: 85. Ctenoplusia agnata (NCBI accession number GU477713.1, protein accession number ADV17598.1, Wu M, et al (2011) Genetica 139 :149-54. "Cloning" with an open reading frame encoding the putative transposase of SEQ ID NO: 29. and characterization of piggyBac-like elements in lepidopteran insects"), and Macrostomum lignano (also described in "SEQ. Orussus abietinus (NCBI Accession number XM_012421754, protein accession number XP_012277177), Eufriesea mexicana (NCBI genome reference number NIVC01003029.1, Protein Accession No. XP_017759329), Spodoptera litura (NCBI Genome Reference No. NC_036206 .1, protein accession number XP_022824855), Vanessa tameamea (NCBI genome reference number NW_020663261), which has an open reading frame encoding the putative transposase of SEQ ID NO: 34 flanked by the putative left end of SEQ ID NO: 94 and the putative right end of SEQ ID NO: 95. 1, Protein Accession No. , protein accession number PSN31819), Onthophagus taurus (NCBI genome reference number NW_019281532.1, Onthophagus taurus (NCBI genome reference number NW_019281689.1, protein accession number Accession No. Session number XP_022913435), Megachile rotundata (NCBI genome reference number NW_003797295, protein accession number ), Xiphophorus maculatus (NCBI Genome Reference Number NC_036460.1, Protein Accession Number , and Oryzias latipes (NCBI Accession No. NC_019868.2, Protein Accession No. We identified a putative transposon with an intact transposase from .

5.2.5.1 Orydias transposase and its corresponding transposon One active transposase and its corresponding transposon identified by transposition activity in yeast was the Orydias transposase, as described in Section 6.1.2. orygius transposase is at least 80% identical, or at least 90% identical, or at least 93% identical, or at least 95% identical, or at least 96% identical, or at least 97% identical to the sequence set forth in SEQ ID NO: 782; or comprises a polypeptide sequence that is at least 98% identical, or at least 99% identical, or 100% identical, and is capable of transposing a transposon from the transposase reporter construct SEQ ID NO: 41, as described in Section 6.1.2. It is. Exemplary non-naturally occurring transposases include the sequences set forth in SEQ ID NOs: 805-908.

Orydias transposase may be provided as a protein as part of a gene introduction system, or may be provided as a polynucleotide encoding Orydias transposase. The polynucleotide can be expressed in the target cell. If provided as a polynucleotide, the orydias transposase may be provided as DNA or mRNA. When provided as DNA, the open reading frame encoding the transposase is preferably a promoter that is activated in the target cell such that the transposase can be expressed in the target cell, e.g. eukaryotic cells, vertebrates. operably linked to heterologous regulatory elements, including promoters that are activated in cellular or mammalian cells. When provided as mRNA, the mRNA is preferably operable by an active heterologous promoter, e.g., the T7 promoter, in the in vitro transcription system used to prepare the mRNA. It may also be prepared in vitro from ligated DNA molecules.

Orygias transposon contains a heterologous polynucleotide sandwiched between a left transposon end containing a left ITR having the sequence SEQ ID NO: 7 and a right transposon end containing a right ITR having the sequence SEQ ID NO: 8, and the far end of each ITR. It is characterized by a position immediately adjacent to the target sequence. Here and elsewhere, when an inverted repeat is defined by a sequence containing a nucleotide defined by an ambiguity code, the identity of that nucleotide can be selected independently in the two repeats. A preferred target sequence is 5'-TTAA-3', although other available target sequences may be used. Preferably, the target sequence on one side of the transposon is a direct repeat of the target sequence on the other side of the transposon. The left transposon end may further comprise an additional sequence proximal to the ITR, such as a sequence at least 90% identical, or 100% identical, to a sequence selected from SEQ ID NO: 5, 11 or 12. The right transposon end may further comprise an additional sequence proximal to the ITR, such as a sequence at least 90% identical, or 100% identical to a sequence selected from SEQ ID NO: 6, 13, 14, or 15. good. The structure of a typical Orydias transposon is shown in Figure 1. The orygias transposon can be transposed, for example, by a transposase having a polypeptide sequence of SEQ ID NO: 782, as encoded by a polynucleotide having a sequence of SEQ ID NO: 780 operably linked to a Gal promoter.

A transposon end containing an ITR and a target sequence may be added to the end of a heterologous polynucleotide sequence to create a synthetic Orydias transposon that can be efficiently transferred into a target eukaryotic genome by an Orydias transposase. For example, SEQ ID NOs: 1, 16, and 17 each have a left 5'-TTAA-3' target sequence followed by a left transposon ITR, and further include a heterologous polynucleotide such that the target sequence is distal to the heterologous polynucleotide. Additional end sequences can be followed that can be added to one side of the polynucleotide to generate a synthetic origin transposon. SEQ ID NOs: 2, 18, 19 and 20 each have an additional end sequence followed by the right transposon ITR sequence and also on the other side of the heterologous polynucleotide such that the target sequence is distal to the heterologous polynucleotide. A right 5'-TTAA-3' target sequence can be added to generate a synthetic origias transposon. Although the previous transposon end sequence contains 5'-TTAA-3' as a target sequence, this target sequence may be removed from both ends of the synthetic origin transposon and replaced with an alternative target sequence.

Orydias transposase recognizes synthetic Orydias transposons. They excise the transposon from the first DNA molecule by cleaving the DNA at the target sequence at the left end of the first transposon end and at the right end of the second transposon end, The cut ends of the molecule are recombined, leaving a single copy of the target sequence. The excised transposon sequences (including the foreign DNA between the transposon ends) are integrated by transposases into the target sequence of a second DNA molecule, such as the genome of a target cell. A cell whose genome includes a synthetic orydias transposon is one embodiment of the invention.

5.2.5.2 Orygias transposase is active in mammalian cells The piggyBac transposase of L. lupermoss has been shown to be active in a large variety of eukaryotic cells. In section 6.1.2 we show that Orydia transposase is able to transfer the corresponding transposon into the genome of the yeast Saccharomyces cerevisiae. In section 6.1.3 we show that the orydias transposase is able to transfer the corresponding transposon into the genome of mammalian CHO cells. These results provide evidence that the Orydias transposase, like other known active piggyBac-like transposases, is active in transposing the corresponding transposon into the genome of most eukaryotic cells. Although the orydias transposase exhibits activity in a wide range of eukaryotic cells, the naturally occurring open reading frame encoding the orydias transposase (denoted by SEQ ID NO: 781) is unique because optimal codon usage varies widely between cell types. , it is unlikely that it would be expressed successfully in a similarly wide range of cells. It is therefore advantageous to use sequences other than naturally occurring sequences to encode transposases, in other words to use the codon preferences of the cell type in which expression is desired. Similarly, promoters and other control sequences are selected to be active in the cell type in which expression occurs. Advantageous polynucleotides for the expression of orygius transposase have at least 2, 5, 10, 20, 30, 40 or 50 polynucleotides with respect to SEQ ID NO: 781 in the corresponding position between the polynucleotide and SEQ ID NO: 781. Optionally, codons in the polynucleotide at corresponding positions are selected for expression in mammalian cells, including differences in synonymous codons. In the exemplary polynucleotide sequence of the orydia transposase having the polypeptide sequence of SEQ ID NO: 782, differences in synonymous codons for SEQ ID NO: 781 at corresponding positions between the polynucleotide and SEQ ID NO: 781 result in expression in mammalian cells. and is given as SEQ ID NO: 780. Polynucleotides may be DNA or mRNA.

5.2.6 Highly Active Orygias Transposase Individual advantageous mutations can be described, for example, in “DNA shuffling” or in US Pat. -7-16 "Engineering proteinase K using machine learning and synthetic genes") can be combined in a variety of different ways. Transposases with modified activity, either for activity against a new target sequence or for increased activity against an existing target sequence, can be detected using the selection scheme described herein using the appropriate corresponding transposon. variations (e.g. Section 6.1.6).

Alignments of known active piggyBac-like transposases may be used to identify amino acid changes that are likely to result in enhanced activity. Because transposases are often deleterious to the host, they tend to accumulate mutations that inactivate them. However, the mutations that accumulate in different transposases are different, and each occurs with random probability. A consensus sequence can be obtained from sequence alignment, which can be used to improve activity (Ivics et al, 1997. Cell 91: 501-510. "Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells." Known active piggyBac-like transposases were sequenced using the CLUSTAL algorithm, and the amino acids found at each position were listed. This diversity is shown in Table 1 in comparison to the Orygias transposase (related to SEQ ID NO: 782), where the amino acids shown in column C are found at equivalent positions in the alignment in known active piggyBac-like transposases. Therefore, this is considered an acceptable change in the transposase. Column D shows the amino acid changes found in known active piggyBac-like transposases other than the Orydias transposase; this position is well conserved in other transposase sets, but the amino acid in the sequence of the Orydias transposase is an outlier. It is. When the position shown in column A is mutated to the amino acid shown in column D, the sequence of Orydias transposase changes toward the consensus, and therefore transposase activity is particularly likely to be enhanced.

60 amino acid substitutions were selected from column D of Table 1 in the transposase SEQ ID NO: 782. Replacements are E22D, D82K, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, G172A, R175K, K177N, G178R, L200R, T202R, I206L, I210L, N214D, W2 37F, V251L, V253I, V258L , M270I, I281F, A284L, M319L, G322P, L323V, H326R, F333W, Y337I, L361I, V386I, M400L, T402S, H404D, S408E, L409I, D422F, K435Q, Y440M, F455Y, V4 58L, D459N, S461A, A465S, V467I , L468I, W469Y, A512R, A514R, V515I, S524P, R548K, D549K, D550R, S551R, and N562K. Genes encoding Orydia transposase variants containing combinations of these substitutions were synthesized and tested for transposase activity as described in section 6.1.6.

In addition to the naturally occurring sequence SEQ ID NO: 782, we have designed more than 70 non-naturally occurring transposase variants with excision or transposition activity. Exemplary sequences of active non-naturally occurring transposase variants are provided as SEQ ID NOs: 816-877. Orydia transposase variants with enhanced excision activity compared to transposition activity are provided as SEQ ID NOs: 805-815.

therefore, is not a naturally occurring sequence, but is at least 99% identical, or at least 98% identical, or at least 97% identical, or at least 96% identical, or at least 95% identical, or at least 90% identical to SEQ ID NO: 782; orygius transposase that is at least 80% identical. Such variants may retain partial activity of the transposase of SEQ ID NO: 782 (as determined by either or both transposition and/or excision activity) and may retain the It can be functionally equivalent to the transposase of SEQ ID NO: 782, or it can have enhanced activity relative to the transposase of SEQ ID NO: 782 in transposition, excision activity, or both. Such variants include mutations shown herein to increase metastasis and/or resection, mutations shown herein to be neutral with respect to metastasis and/or resection, and mutations shown herein to be neutral with respect to metastasis and/or resection. and/or may contain mutations detrimental to integration. Preferred variants include mutations shown to be neutral or mutations shown to enhance metastasis and/or resection. Some such variants lack mutations shown to be deleterious to metastasis and/or resection. Some such variants include only mutations shown to enhance metastasis, only mutations shown to enhance resection, or mutations shown to enhance both metastasis and resection. Including things.

Enhanced activity refers to an activity (eg, transposition or excision activity) that is greater than the activity of the reference transposase from which the variant is derived by more than experimental error. The activity can be increased, for example, by a factor of 1.2, 1.5, 2, 5, 10, 15, 20, 50 or 100 times that of the reference transposase. The enhanced activity can be in the range of, for example, 1.2-100 times, 2-50 times, 1.5-50 times or 2-10 times that of the reference transposase. Activity here and elsewhere can be measured as demonstrated in the Examples.

Functional equivalence means that the variant transposase is capable of mediating transposition and/or excision of the same transposon with the same efficiency (within experimental error) as the reference transposase.

Furthermore, variant sequences of SEQ ID NO: 782 can be created by combining two, three, four, or five or more substitutions selected from column D of Table 1. By combining beneficial substitutions, such as those shown in column D of Table 1, highly active variants of SEQ ID NO: 782 can be obtained. Preferred highly active transposases include amino acids 22, 124, 131, 138, 149, 156, 160, 164, 167, 171, 175, 177, 202, 206, 210, 214, 253, comprising an amino acid substitution at a position selected from 258, 281, 284, 361, 386, 400, 408, 409, 455, 458, 467, 468, 514, 515, 524, 548, 549, 550, and 551; (see Section 6.1.6).
Preferably, the substitutions are those shown in column C or D of Table 1. Advantageous high activity orydia transposases are E22D, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, R175K, K177N, T202R, I206L, I210L, N214D, V253I, V258L, I28 1F, A284L, L361I , V386I, M400L, S408E, L409I, F455Y, V458L, V467I, L468I, A514R, V515I, S524P, R548K, D549K, D550R, and S551R (relative to SEQ ID NO: 782). Some highly active orydias transposases may further include a heterologous nuclear localization sequence.

Some engineered origin transposases may have greater excision activity compared to the transposase activity of the transposase. Advantageous origin transposases with high activity for excision include amino acid substitutions at positions selected from amino acids 156, 164, 167, 171, 175, 177, 284, and 455 relative to the sequence of SEQ ID NO: 782, e.g. May include amino acid substitutions selected from L156T, Y164F, I167L, A171T, R175K, K177N, A284L, and F455Y. By combining such substitutions, an origin transposase with stronger resection activity than translocation activity may be designed. Exemplary transposases with high activity for excision include sequences selected from SEQ ID NOs: 805-815.

Preferred highly active transposases have amino acid sequences other than those of naturally occurring proteins (e.g., are not transposases whose amino acid sequence comprises SEQ ID NO: 782), and which have an amino acid sequence of any of SEQ ID NOs: 805 to 877. At least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids 22, 124, 131, 138, 149, 156 to SEQ ID NO: 782 , 160, 164, 167, 171, 175, 177, 202, 206, 210, 214, 253, 258, 281, 284, 361, 386, 400, 408, 409, 455, 458, 467, 468, 514, 515 , 524, 548, 549, 550, and 551. Preferably, the highly active orydias transposase is E22D, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, R175K, K177N, T202R, I206L, I210L, N214D for the sequence of SEQ ID NO: 782. , V253I, V258L, I281F, A284L, L361I, V386I, M400L, S408E, L409I, F455Y, V458L, V467I, L468I, A514R, V515I, S524P, R548K, D549K, D550R, and S551R amino acid substitutions, or these or any combination of substitutions thereof, including at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all mutations of .

Methods for producing transgenic cells using naturally occurring or highly active transposases are an aspect of the invention. The method for producing transgenic cells comprises the steps of (i) introducing into a eukaryotic cell a naturally occurring or highly active orydia transposase (as a protein or as a polynucleotide encoding the transposase) and a corresponding orydia transposase; include. The production of a transgenic cell may further include the step of (ii) identifying a cell in which the orydias transposon has been integrated into the eukaryotic genome. The step of identifying cells in which the Orydias transposon has been integrated into the genome of the eukaryotic cell may include the step of selecting eukaryotic cells for a selectable marker encoded by the Orydias transposon. The selectable marker may be any selectable polypeptide, including those described herein.

The activity of the transposase is determined by the fusion of a nuclear localization signal (NLS) to the N-terminus, C-terminus, both the N-terminus and C-terminus, or an internal region of the transposase protein, as long as the activity of the transposase is retained. It can also be increased by A nuclear localization signal or sequence (NLS) is an amino acid sequence that directly or indirectly "tags" or facilitates the interaction of a protein with a nuclear transport protein for import into the cell nucleus. The nuclear localization signal (NLS) used can include consensus NLS sequences, viral NLS sequences, cellular NLS sequences, and combinations thereof.

Additionally, the transposase may be fused with other protein functional domains. Such protein functional domains can include DNA binding domains, flexible hinge regions that can facilitate fusion of one or more domains, and combinations thereof. Fusions can be made to either the N-terminus, C-terminus, or internal regions of the transposase protein, as long as transposase activity is retained. Fusion to a DNA binding domain can be used to direct the Orydia transposase to a particular genomic locus or genetic locus. DNA binding domains include helix-turn-helix domains, zinc finger domains, leucine zipper domains, TALE (transcription activator-like effector) domains, CRISPR-CAS proteins, or helix-loop-helix domains. Specific DNA-binding domains may include the Gal4 DNA-binding domain, the LexA DNA-binding domain, and the Zif268 DNA-binding domain. The flexible hinge region can include glycine/serine linkers and variants thereof.

5.3 Kits The present invention also provides kits comprising an Orydias transposase as a protein or encoded by a nucleic acid, and/or an Orydias transposon, or in combination with an Orydias transposon, as a protein or by a nucleic acid as described herein. The present invention features a kit comprising a gene transfer system as described herein, including an encoded transposase, optionally accompanied by a pharmaceutically acceptable carrier, adjuvant or vehicle, and optionally instructions for use. Any of the components of the kit of the invention may be administered and/or transfected to the cells in a subsequent order or in parallel, for example prior to or simultaneously with the administration and/or transfection of the Orydias transposon. or subsequently, the orydia transposase protein or its encoding nucleic acid may be administered and/or transfected into the cells as defined above. Alternatively, the orydias transposon may be transfected into the cell as defined above prior to, simultaneously with, or subsequent to transfection of the orydias transposase protein or its encoding nucleic acid. If transfections are carried out in parallel, both components are preferably provided in separate formulations and/or mixed directly with each other before administration, in order to avoid transfer before transfection. Furthermore, the administration and/or transfection of at least one component of the kit may be carried out in a staggered mode, for example by administering this component multiple times.

6. EXAMPLES The following examples are illustrative of the methods, compositions, and kits disclosed herein and are not to be construed as limiting in any way. Various equivalents will become apparent from the examples below. Such equivalents are also intended to be part of the invention disclosed herein.

6.1 New transposases
6.1.1 Measuring Transposase Activity As described in Section 5.2.5, the frequency of transposition of active transposases can be measured using a system in which transposons interrupt selectable markers. A transposase reporter polynucleotide was constructed in which the open reading frame of the yeast Saccharomyces cerevisiae URA3 open reading frame was interrupted by the yeast TRP1 open reading frame operably linked to a promoter and terminator for expression in yeast Saccharomyces cerevisiae. The TRP1 gene is flanked by putative transposon ends with a 5'-TTAA-3' target site, and when the putative transposon is excised, one copy of the 5'-TTAA-3' target site remains and the URA3 open reading frame was now reconfigured accurately. The yeast transposase reporter strain was constructed by integrating a transposase reporter polynucleotide into the URA3 gene of a haploid yeast strain that supports LEU2 and TRP1, resulting in LEU2-, URA3-, and TRP1+.

The transposase was tested for its ability to transfer the transposon containing the TRP1 gene from within the URA3 open reading frame. Each open reading frame encoding a putative transposase was cloned into a Saccharomyces cerevisiae expression vector containing a 2 micron origin of replication and the LEU2 gene expressible in Saccharomyces. The open reading frame of each transposase was operably linked to the Gal1 promoter. The cloned transposase open reading frame was transformed into a yeast transposase reporter strain and plated on minimal medium lacking leucine. After 2 days, all LEU+ colonies were collected by scraping the plates. After 4 hours of incubation with galactose to induce the Gal promoter, cells were plated on three different plates: a plate lacking only leucine, a plate lacking leucine and uracil, and a plate lacking leucine, uracil, and tryptophan. These plates were cultured for 2-4 days, and the colonies on each plate were counted to determine the number of viable cells, the number of transposon excision events, and the number of transposon excision and reintegration (ie, transposition events), respectively.

6.1.2 Identification of active Orydias PIGGYBAC-like transposases As described in section 5.2.5, we identified 21 putative piggyBac-like transposases from Genbank that are at least 20% identical to the piggyBac transposase from Trichoplusia ni. . This transposase appears to contain the DDDE motif characteristic of active piggyBac-like transposases. Flanking DNA sequences were analyzed and confirmed the presence of an inverted repeat sequence immediately adjacent to the 5'-TTAA-3' target sequence characteristic of piggyBac transposition. From this flanking sequence, we obtained putative left and right transposon end sequences containing the sequence between the 5'-TTAA-3' target sequence and the open reading frame encoding the putative transposase. These transposon ends were incorporated into a transposase reporter construct constructed as described in Section 6.1.1 and integrated into the Saccharomyces cerevisiae genome to generate a transposase reporter strain. Transposase sequences corresponding to each reporter strain were synthesized by back translation and cloned into a Saccharomyces cerevisiae expression vector to transform the reporter strain. Transposase activity was measured as described in section 6.1.1.

No resection or metastasis was observed in the following 20 combinations. Reporter construct SEQ ID NO: 48 (including putative left transposon end SEQ ID NO: 68 and putative right transposon end SEQ ID NO: 69), transposase SEQ ID NO: 21, reporter construct SEQ ID NO: 49 (including putative left transposon end SEQ ID NO: 70 and putative right transposon end SEQ ID NO: 71) and transposase SEQ ID NO: 22, reporter construct SEQ ID NO: 50 (including putative left transposon end SEQ ID NO: 72 and putative right transposon end SEQ ID NO: 73), transposase SEQ ID NO: 23, reporter construct SEQ ID NO: 51 (including putative left transposon end SEQ ID NO: 73), SEQ ID NO: 74 and putative right transposon end SEQ ID NO: 75) and transposase SEQ ID NO: 24; reporter construct SEQ ID NO: 52 (comprising putative left transposon end SEQ ID NO: 76 and putative right transposon end SEQ ID NO: 77); Reporter construct SEQ ID NO: 53 (including putative left transposon end SEQ ID NO: 78 and putative right transposon end SEQ ID NO: 79), transposase SEQ ID NO: 26, reporter transposase SEQ ID NO: 54 (including putative left transposon end SEQ ID NO: 80 and putative right transposon end SEQ ID NO: 81) and transposase SEQ ID NO: 27, reporter construct SEQ ID NO: 55 (including putative left transposon end SEQ ID NO: 82 and putative right transposon end SEQ ID NO: 83), transposase SEQ ID NO: 28, reporter construct SEQ ID NO: 56 (including putative left transposon end SEQ ID NO: 83), SEQ ID NO: 84 and putative right transposon end SEQ ID NO: 85) and transposase SEQ ID NO: 29, reporter construct SEQ ID NO: 57 (including putative left transposon end SEQ ID NO: 86 and putative right transposon end SEQ ID NO: 87) and transposase SEQ ID NO: 30. Reporter construct SEQ ID NO: 58 (including putative left transposon end SEQ ID NO: 88 and putative right transposon end SEQ ID NO: 89), transposase SEQ ID NO: 31, reporter construct SEQ ID NO: 59 (including putative left transposon end SEQ ID NO: 90 and putative right transposon end SEQ ID NO: 91) and transposase SEQ ID NO: 32, reporter construct SEQ ID NO: 60 (including putative left transposon end SEQ ID NO: 92 and putative right transposon end SEQ ID NO: 93), transposase SEQ ID NO: 33, reporter construct SEQ ID NO: 61 (including putative left transposon end SEQ ID NO: 93), transposase SEQ ID NO: 34, reporter construct SEQ ID NO: 62 (comprising putative left transposon end SEQ ID NO: 96 and putative right transposon end SEQ ID NO: 97) and transposase SEQ ID NO: 35. , reporter construct SEQ ID NO: 63 (including putative left transposon end SEQ ID NO: 98 and putative right transposon end SEQ ID NO: 99) and transposase SEQ ID NO: 36, reporter construct SEQ ID NO: 64 (including putative left transposon end SEQ ID NO: 100 and putative right transposon end) transposase SEQ ID NO: 37, reporter construct SEQ ID NO: 65 (comprising putative left transposon end SEQ ID NO: 102 and putative right transposon end SEQ ID NO: 103), transposase SEQ ID NO: 38, reporter construct SEQ ID NO: 66 (predicted left transposon end SEQ ID NO: 103), transposon end SEQ ID NO: 104 and putative right transposon end SEQ ID NO: 105) and transposase SEQ ID NO: 39, reporter construct SEQ ID NO: 67 (including putative left transposon end SEQ ID NO: 106 and putative right transposon end SEQ ID NO: 107) and transposase SEQ ID NO: 40. Although it is simple to computationally recognize sequences with homology to the Trichoplusia ni piggyBac transposase, most of these sequences have intact terminal repeats and the transposase contains the DDDE motif found in active piggyBac-like transposases. However, this is consistent with reports in the literature that it is metastatically inactive. Therefore, in order to identify novel active piggyBac-like transposases and transposons, it is necessary to measure excision and transposition activities.

One of the transposases that showed good activity in excising its corresponding transposon from the reporter construct (as indicated by the appearance of URA+ colonies) and transferring the TRP gene in the transposon to another genomic location in the reporter strain of Saccharomyces cerevisiae One was transposase SEQ ID NO: 782. Transposase SEQ ID NO: 782 was able to transpose the transposon from reporter construct SEQ ID NO: 41. This is shown in Table 2. The number of excision events as measured by the appearance of URA+ colonies is shown in column G. The number of full metastasis events as measured by the appearance of URA+ TRP+ colonies is shown in column H.

6.1.3 Orygias transposase is active in mammalian cells
PiggyBac-like transposases transfer corresponding transposons into the genomes of eukaryotic cells, including yeast cells such as Pichia pastoris and Saccharomyces cerevisiae, and mammalian cells such as human embryonic kidney (HEK) cells and Chinese hamster ovary (CHO) cells. can be done. To examine the activity of piggyBac-like transposases in mammalian cells, a glutamine synthetase having the polypeptide sequence set forth in SEQ ID NO: 129, containing a transposon end and operably linked to regulatory elements conferring weak glutamine synthetase expression. A transgenic polynucleotide was constructed that further contains a selectable marker encoding. Here, the sequence of glutamine synthetase and its associated control elements is shown as SEQ ID NO: 172. The transgenic polynucleotide further includes open reading frames encoding the heavy and light chains of the antibody, each operably linked to a promoter and a polyadenylation signal sequence. The transgenic polynucleotide (having SEQ ID NO: 108) contains the ITR sequence shown in SEQ ID NO: 9, which is an embodiment of SEQ ID NO: 7, immediately after the left transposon end containing the 5'-TTAA-3' target integration sequence. Contains the originating left transposon end. The transgenic polynucleotide further comprises an origin right transposon end with an ITR sequence shown in SEQ ID NO: 10 (which is an embodiment of SEQ ID NO: 8) and a 5'-TTAA-3' target integration sequence immediately thereafter. Two originating transposon ends were placed on either side of a heterologous polynucleotide containing a glutamine synthetase selectable marker and an open reading frame encoding the heavy and light chains of the antibody. The left transposon end further contained the sequence shown in SEQ ID NO: 5 immediately adjacent to the left ITR and proximal to the heterologous polynucleotide. The right transposon end further contained the sequence shown in SEQ ID NO: 6 immediately adjacent to the right ITR and proximal to the heterologous polynucleotide.

The transgenic polynucleotide was transfected into CHO cells lacking a functional glutamine synthetase gene. Cells were electroporated with 25 μg of transgenic polynucleotide DNA with or without co-transfection with 3 μg of DNA containing the gene encoding the transposase operably linked to the human CMV promoter and polyadenylation signal sequence. Transfection was carried out by transfection. After electroporation, they were cultured for 48 h in medium containing 4 mM glutamine and then diluted to 300,000 cells per ml in medium lacking glutamine. Cells were replaced with fresh medium without glutamine every 5 days. Cell viability for each transfection was determined at various time points post-transfection using a Beckman-Coulter Vi-Cell. The total number of viable cells was also determined with the same device. The results are shown in Table 3.

As shown in Table 3, the survival rate of cells introduced with the transgenic polynucleotide but not transposase decreased to about 27% by day 12 after introduction (column B). The total number of viable cells decreased to less than 50,000 cells per ml within 7 days (column C). For viable cell numbers below this density, viability measurements will be inaccurate. Culture did not recover. On the other hand, when the transgenic polynucleotide of SEQ ID NO: 108 was co-introduced with Orydias transposase SEQ ID NO: 782, the cells recovered to a survival rate of over 90% within 10 days (column D of Table 3), and at that time, the cells recovered to a survival rate of more than 90%. The density was over 2 million/ml (column E of Table 3). This indicates that transgenic polynucleotides containing left and right Orydias transposon ends can be efficiently introduced into the genome of mammalian target cells by the corresponding Orydias transposase.

A recovered pool of CHO cells containing a piggyBac-like transposon integrated into the genome was cultured in a 14-day fed-batch using Sigma Advanced Fed Batch medium. The antibody titer in the culture supernatant was measured in octets. Table 4 shows the titers measured on days 7, 10, 12, and 14 of fed-batch culture. Antibody titers from cells into which the transgenic polynucleotide having SEQ ID NO: 108 was co-introduced and integrated with Orydias transposase SEQ ID NO: 782 reached approximately 2 g/L after 14 days. This suggests that the orydias transposons and their corresponding transposases, described in Section 5.2.5, are active in mammalian cells and are useful for the development of protein-expressing cell lines and the engineering of genomes in mammalian cells. It turned out to be a type transposon/transposase system.

6.1.4 Messenger RNA encoding the Orygius transposase is active in mammalian cells The transgenic polynucleotide with SEQ ID NO: 108, the composition of which is described in Section 6.1.3, was further tested to demonstrate that the corresponding transposase is active in mammalian cells. We investigated whether synthetic Orydias transposons integrate into the genome of mammalian cells when provided in the form of

mRNA encoding the transposase was prepared by in vitro transcription using T7 RNA polymerase. This mRNA contained a 5' sequence, SEQ ID NO: 109, preceding the sequence encoding the open reading frame, and a 3' sequence, SEQ ID NO: 110, following the last stop codon of the open reading frame. This mRNA had an anti-reverse cap analog 3'-O-Me-m ⁷ G(5')ppp(5')G. DNA molecules containing a transposase-encoding sequence operably linked to a heterologous promoter active in vitro are useful for the preparation of transposase mRNA. Isolated mRNA molecules containing transposase-encoding sequences are useful for integrating the corresponding transposon into a target genome.

Gene transfer polynucleotide 354498 having SEQ ID NO: 108 contains a selectable marker encoding a glutamine synthetase having a polypeptide sequence shown by SEQ ID NO: 129, and is encoded by a DNA sequence shown by SEQ ID NO: 134 and is a weak glutamine synthetase. was operably linked to a control element that conferred expression of. Here, the sequence of glutamine synthetase and its associated control elements is shown by SEQ ID NO: 172. The transgenic polynucleotide SEQ ID NO: 108 further contained open reading frames encoding the heavy and light chains of the antibody, each operably linked to a promoter and a polyadenylation signal sequence. Gene transfer polynucleotide SEQ ID NO: 108 further included an origin left transposon end having the sequence shown in SEQ ID NO: 1 and an origin right transposon end having the sequence shown in SEQ ID NO: 2.

mRNA encoding Orydias transposase was prepared by in vitro transcription using T7 RNA polymerase. This mRNA consists of the 5' sequence SEQ ID NO: 109 preceding the open reading frame, the open reading frame encoding orygias transposase (amino acid sequence SEQ ID NO: 782, nucleotide sequence SEQ ID NO: 780), and the end of the open reading frame. It contained the 3' sequence SEQ ID NO: 110 following the stop codon. The transgenic polynucleotide SEQ ID NO: 108 was transfected into CHO cells that do not have a functional glutamine synthetase gene. Cells were transfected by electroporation. 25 μg of transgenic polynucleotide DNA was co-introduced with 3 μg of mRNA containing an open reading frame encoding the corresponding transposase (amino acid sequence SEQ ID NO: 782, nucleotide sequence SEQ ID NO: 780). After electroporation, cells were cultured for 48 h in medium containing 4 mM glutamine and subsequently diluted to 300,000 cells per ml in medium lacking glutamine. Cells were replaced with fresh glutamine-free medium every 5 days. Cell viability for each transfection was measured at various time points post-transfection using a Beckman-Coulter Vi-Cell. The total number of viable cells was also determined with the same device. The results are shown in Table 5.

When the transgenic polynucleotide having SEQ ID NO: 108 was co-introduced with mRNA encoding Orydias transposase SEQ ID NO: 782, the survival rate decreased to approximately 28% on the 9th day after introduction (Table 5B row); The density of living cells was approximately 40,000/ml (Table 5C row). Thereafter, cell viability and viable cell density increased, and by day 28 after introduction, the survival rate was over 96% and the number of viable cells was over 3 million per ml. This indicates that transgenic polynucleotides containing left and right Orygius transposon ends can be efficiently introduced into the genome of mammalian target cells by co-introducing mRNA encoding the corresponding Orygias transposase. .

6.1.5 Orydias transposon end sequences active in mammalian cells When Orydias transposons were first tested, the entire sequence between the 5'-TTAA-3' target sequence and the transposase open reading frame was used as the transposon end. However, for other piggyBac-like sequences, we found that such complete sequences are generally not required for transposition activity. Therefore, we created a synthetic Orydias transposon with a truncated end and investigated whether it could be transposed by Orydias transposase. The heterologous polynucleotide having SEQ ID NO: 42 encoded a glutamine synthetase having the polypeptide sequence set forth in SEQ ID NO: 130 and was operably linked to a control element that conferred weak glutamine synthetase expression as a selectable marker. On one side of the heterologous polynucleotide was a left origin transposon end containing a 5'-TTAA-3' integrated target sequence immediately followed by a transposon ITR sequence having SEQ ID NO: 9, an embodiment of SEQ ID NO: 7. . On the other side of the heterologous polynucleotide is a right origin transposon end containing a 5'-TTAA-3' integrated target sequence immediately following a transposon ITR sequence having SEQ ID NO: 10 (which is an embodiment of SEQ ID NO: 8). there were. The transposon further contained additional sequences selected from SEQ ID NOs: 5, 11 and 12 immediately adjacent to (following) the left transposon ITR sequence. The transposon further contained additional sequences selected from SEQ ID NO: 6, 13, 14 and 15 immediately adjacent to (preceding) the ITR sequence of the right transposon. The transposon was transfected into CHO cells that lack a functional glutamine synthetase gene. Cells were transfected by electroporation. Transfect cells with 25 μg of transgenic polynucleotide DNA and optionally co-incubate cells with 3 μg of mRNA containing an open reading frame encoding the corresponding transposase (amino acid sequence SEQ ID NO: 782, nucleotide sequence SEQ ID NO: 780). Introduced. After electroporation, they were cultured for 48 h in medium containing 4 mM glutamine and then diluted to 300,000 cells per ml in medium lacking glutamine. Cells were replaced with fresh medium without glutamine every 5 days. Cell viability of each transfection was measured at various time points post-transfection using Beckman-Coulter Vi-Cell. The total number of viable cells was also determined with the same device. The results are shown in Table 6.

Columns B and C of Table 6 show the case where cells were transfected with a transposon containing a truncated left transposon end with SEQ ID NO: 11 and a full-length right transposon end with SEQ ID NO: 6 in the absence of transposase. shows a decrease in cell viability and viable cell density. In this experiment, it was confirmed that both cell viability and viable cell density were reduced. On the other hand, when the same transposon was co-introduced with mRNA encoding the Orydias transposer, cell viability and viable cell density initially decreased, but began to recover by day 14, and between days 19 and 24. completely recovered (Table 6, columns C and D). Similar results were also obtained when cells were transfected with a transposon containing a truncated left transposon end with SEQ ID NO: 12 and a full-length right transposon end with SEQ ID NO: 6 (Table 6). Compare columns E and F with columns G and H, respectively). Similar results were also obtained when cells were transfected with transposons containing a full-length right transposon end with SEQ ID NO: 5 and a truncated right transposon end with SEQ ID NO: 13 (I and I in Table 6). Compare column J with column K and L respectively). Similar results were also obtained when cells were transfected with a transposon containing a full-length left transposon end with SEQ ID NO: 5 and a truncated right transposon end with SEQ ID NO: 14 (Table 6 Compare columns M and N with columns O and P, respectively). Similar results were also obtained when transposons containing a full-length left transposon end with SEQ ID NO: 5 and a truncated right transposon end with SEQ ID NO: 15 were introduced into cells (column Q in Table 6). and compare R, S, and T columns, respectively). This means that in addition to the integrated target sequence immediately adjacent to the transposon ITR sequence with SEQ ID NO: 7, the originating synthetic transposon left transposon end is selected from SEQ ID NO: 5, 11 and 12 immediately adjacent to the left transposon ITR sequence. and that the origias synthetic transposon right transposon end may further include additional sequences selected from SEQ ID NO: 6, 13, 14 and 15 immediately adjacent to the right transposon ITR sequence of SEQ ID NO: 8. Show good.

6.1.6 Production of highly active orydias transposase For the naturally occurring orydias transposase sequence shown by SEQ ID NO: 782, orydias transposase mutations leading to either increased transposition activity or increased excision activity are identified. To this end, we analyzed the CLUSTAL alignment of active piggyBac-like transposases. Column C of Table 1 shows the amino acids found in active piggyBac-like transposases for each position of the Orydias transposase (positions shown in column A of Table 1). The amino acids present in the orydia transposase shown in SEQ ID NO: 782 are shown in column B of Table 1. Because transposases are often deleterious to the host, mutations that inactivate transposases tend to accumulate. The mutations that accumulate in different transposases are different, and each occurs with random probability. Consensus sequences can therefore be used to approximate the ancestral sequence before the accumulation of deleterious mutations. Because it is difficult to accurately calculate ancestral sequences from the small number of extant sequences, we focused on positions where active transposases are more highly conserved and where the consensus amino acids differ from those of orydias transposases. We reasoned that we might be able to increase the activity of Orydias transposase by mutating these amino acids to consensus amino acids found in other active transposases. These useful amino acid substitution candidates are shown in column D of Table 1.

6.1.6.1 First set of Orygias transposase variants
E22D, D82K, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, G172A, R175K, K177N, G178R, L200R, T202R, I206L, I210L, N214D, W237F, V251L, V253I, V258L, M270I, I281F, A284L, M319L, G322P, L323V, H326R, F333W, Y337I, L361I, V386I, M400L, T402S, H404D, S408E, L409I, D422F, K435Q, Y440M, F455Y, V458L, D459 N, S461A, A465S, V467I, L468I, A set of 95 polynucleotides encoding a variant orydia transposase comprising one or more substitutions selected from W469Y, A512R, A514R, V515I, S524P, R548K, D549K, D550R, S551R, and N562K. Each substitution was represented at least five times in the set of 95 variants, maximizing the number of different pairwise combinations of substitutions so that each substitution was tested in as many different sequence contexts as possible. The gene for each variant was cloned into a vector containing a leucine selectable marker. Each gene encoding a transposase variant was operably linked to the Saccharomyces cerevisiae Gal-1 promoter. Each of these variants was then individually transformed into a Saccharomyces cerevisiae strain containing a chromosomally integrated copy of SEQ ID NO: 41 as described above. After 48 hours, cells were scraped from the plates into minimal medium lacking leucine and containing galactose as the carbon source. The A600 of each culture was adjusted to 2. After 4 hours of incubation in galactose to induce transposase expression, 1:1000 diluted aliquots were plated on medium lacking leucine, uracil, and tryptophan (to count translocations); Plated on medium lacking uracil (counting excisions) and plated 25,000-fold diluted aliquots on medium lacking leucine (counting total viable cells). After 2 days, colonies were counted and metastasized (=number of cells on -leu-ura-trp medium ÷ (25 x number of cells on -leu medium)) and excision (=number of cells on -leu-ura medium ÷ (25 The frequency of cell number)) on ×-leu medium was determined. The results are shown in Table 7. More than 60 of the Orydias transposase variants (having sequences shown in SEQ ID NOs: 816-877) possessed excision or transposition activities of at least 10% of the activity measured for naturally occurring Orydias transposases. Although not as active as natural transposases, all of these transposases are highly active and useful transposases for integrating orydias transposons into the genome of eukaryotic cells. Some orydias transposases with activities shown in Table 7 are highly active for resection compared to the activity of SEQ ID NO: 782. Exemplary transposases with high activity for excision include sequences selected from SEQ ID NOs: 805-815. These are all functional non-naturally occurring transposases.

The effects of sequence changes on resection and metastasis frequencies were investigated in U.S. Patent 8,635,029 and in the paper by Liao et al. "). The mean value and standard deviation of regression weights were calculated for each substituent and are shown in Table 8. The effect of individual substitutions on transposase activity may vary depending on the circumstances (ie, other substitutions present). A positive mean reversion weight indicates that, on average, the substitution has a positive impact on the measured property, considering all the different sequence conditions tested. Incorporating substitutions with positive mean reversion weights into sequences usually results in variants with improved activity (Liao et. al., ibid). A further measure of the context-dependent variability of the effects of substitution is the standard deviation of the regression weights. If the mean reversion weight of a permutation minus the standard deviation of the reversion weight of that permutation is greater than or equal to zero, then the permutation will have a positive effect in most situations. Thirty-one of the 60 substitutions selected by examining changes relative to the consensus of other active piggyBac-like transposases had mean regression weights greater than or equal to 0, subtracting the standard deviation of the resection or metastasis regression weights (E22D, A124C , Q131D, L138V, D160E, Y164F, I167L, A171T, R175K, T202R, I206L, I210L, N214D, V253I, V258L, I281F, A284L, V386I, M400L, S408E, L409I, F455Y, V4 58L, V467I, L468I, A514R, V515I , R548K, D549K, D550R, and S551R (Table 8, columns F and I). Thirty-six substitutions selected by examining changes to the consensus of other active piggyBac-type transposases had mean regression weights greater than 0 (E22D, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, R175K, K177N, T202R, I206L, I210L, N214D, V253I, V258L, I281F, A284L, L361I, V386 I, M400L, S408E, L409I, F455Y, V458L, V467I, L468I, A514R, V515I, S524P, R548K, D549K, D550R, and S551R). Similar substitutions are those in which the properties of the amino acids are conserved; for example, glycine and alanine are a group of "small" amino acids; valine, leucine, isoleucine, and methionine are ``Hydrophobic'' amino acids, phenylalanine, tyrosine, and tryptophan are ``aromatic'' amino acids, aspartic acid and glutamic acid are ``acidic'' amino acids, and asparagine and glutamine are ``amide'' amino acids. Histidine, lysine, and arginine are the "basic" amino acids, and cysteine, serine, and threonine are the "nucleophilic" amino acids. Substitutions at certain amino acid positions within the transposase If beneficial for excision or transposition activity, other substitutions at the same position chosen from the same amino acid group are also likely to be beneficial. For example, replacing the nucleophilic residue serine at position 408 with an acidic residue Since replacing one glutamic acid (S408E) is beneficial, replacing it with the acidic residue aspartic acid (ie S408D) is also considered beneficial. Similarly, replacing the hydrophobic residue valine at position 258 with the hydrophobic residue leucine (V258L) is beneficial, so replacing the hydrophobic residue isoleucine or methionine (i.e., V258I or V258M) is beneficial. ) may also be considered beneficial. Advantageous high activity orydia transposases are amino acids 22, 124, 131, 138, 160, 164, 167, 171, 175, 202, 206, 210, 214, 253, 258, 281 for the sequence SEQ ID NO: 782. , 284, 386, 400, 408, 409, 455, 458, 467, 468, 514, 515, 548, 549, 550, and 551, e.g., E22D, A124C, Q131D, L138V, D160E, Y164F, I167L, A171T, R175K, T202R, I206L, I210L, N214D, V253I, V258L, I281F, A284L, V386I, M400L, S408E, L409I, F455 Y, V458L, V467I, L468I, A514R, There is one or more amino acid substitutions selected from V515I, R548K, D549K, D550R, and S551R, or a similar substitution at one of these positions.

Table 8 also shows that some permutations have positive regression weights for excision, but much less or negative weights for inclusion. This includes the amino acid substitutions L156T, Y164F, I167L, A171T, R175K, K177N, A284L, and F455Y. By combining such substitutions, it is possible to design an origias transposase with stronger resection activity than translocation activity. The highly active and advantageous transposase for excision has amino acid substitutions at one or more positions selected from amino acids 56, 164, 167, 171, 175, 177, 284, and 455 with respect to the sequence SEQ ID NO: 782. for example, one or more amino acid substitutions selected from L156T, Y164F, I167L, A171T, R175K, K177N, A284L, and F455Y, or a similar substitution at one of these positions.

6.1.6.2 Second set of Orygias transposase variants
Liao et al. (2007, BMC Biotechnology 2007, 7:16 doi:10.1186/1472-6750-7-16 "Engineering proteinase K using machine learning and synthetic genes"), U.S. Patent 8,635,029, Sections 5.4.2 and 5.4.3 A positive regression coefficient, weight indicating the relative or absolute contribution to one or more activities of a protein, tested many times in the context of different combinations of other substitutions, as described in , or other values" are usefully incorporated into a protein to obtain a protein "improved in one or more properties, activities, or functions of interest." Based on the substitution weights shown in Table 8, some of the most positive substitutions (L156T, Y164F, I167L, R175K, K177N, I210L, V258L, A284L, V386IL409I, F455Y, V458L, A465S, A514R, and D550R) A set of open reading frames encoding a combined 31 new variants (with sequences shown in SEQ ID NOs: 878-908) was designed. Each substitution was expressed at least five times among the 31 variants, maximizing the number of different pairwise combinations of substitutions so that each substitution was tested in as many different sequence contexts as possible. The open reading frame of each variant was cloned into a vector containing a leucine selectable marker. Each open reading frame encoding a transposase variant was operably linked to the Saccharomyces cerevisiae Gal-1 promoter. Each of these variants was then individually transformed into a Saccharomyces cerevisiae strain containing a chromosomally integrated copy of SEQ ID NO: 41 as described in Section 6.1.6.1. After 48 hours, cells were scraped from the plates into minimal medium lacking leucine and containing galactose as the carbon source. The A600 of each culture was adjusted to 2. Cultures were incubated for 4 h in galactose to induce transposase expression, and then 25,000-fold diluted aliquots were plated on medium lacking leucine, uracil, and tryptophan (to count metastases); Aliquots were plated on medium lacking leucine (to count total viable cells). Two days later, colonies were counted and the frequency of metastasis (=number of cells on -leu -ura -trp medium ÷ (number of cells on -leu medium)) was determined. The results are shown in Table 9.

In addition to the activities of the 31 new Orygias transposase variants, Table 9 also shows the activity of one variant from the first set, which was the most active variant in that set. The activity of the new set of variants was significantly higher than the first set. There are no inactive variants, the lowest observed activity (for SEQ ID NO: 899) is 42% of that of SEQ ID NO: 782, and some variants are similar to naturally occurring orygias transposases (SEQ ID NO: 853, 885, 903, and 905). Preferred transposases include amino acid substitutions selected from L156T, Y164F, I167L, R175K, K177N, I210L, V258L, A284L, V386IL409I, F455Y, V458L, A465S, A514R, and D550R, or similar changes at the same position. include.

Brief Description of the Tables Table 1. Amino acid changes likely to result in enhanced transposase activity Amino acid substitutions with the potential to improve transposase activity were identified as described in Section 5.2.6. Column A shows the position in the Orygius transposase (relative to SEQ ID NO: 782), Column B shows the amino acid in the native protein, and Column C shows the amino acid found in a known active piggyBac-like transposase at the equivalent position in the alignment. , column D identifies amino acid changes found in known active piggyBac-like transposases other than Orygius transposase at positions that are well conserved within the rest of the transposase set but are outliers in the Orygius transposase sequence. show. Mutations in these amino acids are particularly likely to enhance transposase activity. The appearance of multiple amino acid letters in a string means that each of those individual amino acid substitutions is permissible or beneficial, and is not intended to represent a peptide. For example, in the second position, the amino acids T, A, R, D or N are all allowed, so column C includes "TARDN" to indicate this.

Table 2. Transposon excision and transposition in yeast Sources of transposons and transposases are listed in column A. The left sequence with the SEQ ID number shown in column B and the right sequence with the SEQ ID number shown in column C were used to construct the reporter plasmid as described in Section 6.1.2. This reporter plasmid has an insert sequence indicated by the sequence number shown in column D. This reporter plasmid was integrated into the Ura3 gene of the Trp- strain of Saccharomyces cerevisiae. The amino acid sequence shown in the SEQ ID NO: shown in column E was reverse translated, synthesized and cloned into a plasmid containing the Leu2 gene and a 2 micron origin of replication expressible in Saccharomyces cerevisiae. The transposase gene was operably linked to the Gal1 promoter. After transforming the plasmid containing the transposase into the reporter strain and inducing expression, cells were cultured as described in Section 6.1.1. After diluting the induced medium 25,000 times, 100 μl was plated on Leu dropout plates, and after further dilution 100 times, 100 μl was plated on Leu ura or Leu ura trp dropout plates. Column F shows the number of colonies on the leu dropout plate. Column G shows the number of colonies on the leu ura dropout plate (indicating excision of the transposon from the middle of the reporter ura gene). Column H shows the number of colonies on the leu ura trp dropout plate (indicating excision of the transposon from the middle of the reporter ura gene and transposition to another site on the genome).

Table 3. Transfer of transposons into the genome of CHO target cells Cells were transfected with transposon SEQ ID NO: 108 as described in section 6.1.3. The transposon sequence number is shown in the first line. For each transfection, the viability (percentage of cells surviving) and total viable cell density (millions of cells per ml) are shown in adjacent columns, as shown in row 2. Rows 3-17 show these measurements at various time points after transfection, with the number of days elapsed indicated in column A.

Table 4. Antibody production from transposons integrated into the genome of CHO target cells. Cells were transfected with transposons and transposases as described in section 6.1.3. Recovery is shown in Table 3. During the 14-day fed-batch antibody production run, culture supernatants contained the indicated concentrations of antibodies (antibody titers). Column A shows the antibody titer on day 7. Column B shows the antibody titer on day 10. Column C shows the antibody titer on day 12. Column D shows the antibody titer on day 14.

Table 5. Transfer of transposons into the genome of CHO target cells by mRNA-encoded transposase Cells were transfected with transposons and mRNA-encoded transposases as described in Section 6.1.4. Viability (percentage of cells alive) and total viable cell density (millions of cells per ml) are shown in adjacent columns, as shown in row 3. Rows 1-12 show these measurements at various time points after transfection, with the number of days since transfection indicated in column A.

Table 6. Transfer of transposons with truncated terminal sequences into the genome of CHO target cells. Cells were transfected with transposons and optionally mRNA-encoded transposases as described in Section 6.1.5. The transposon sequence number is shown in the first line. Each transposon contains a 5'-TTAA-3' integrated target sequence immediately flanked by the sequence of the ITR having SEQ ID NO: 9 (followed by) the left end sequence having the SEQ ID NO shown in the second line. It contained the left transposon end. The transposon further included SEQ ID NO: 42, an open reading frame encoding a glutamine synthetase selectable marker operably linked to regulatory sequences expressible in mammalian cells. The transposon further comprises a right transposon end comprising a right end sequence having the SEQ ID NO: shown in line 3 immediately adjacent to the transposon ITR sequence having SEQ ID NO: 10 immediately adjacent to the 5'-TTAA-3' integration target sequence. there was. The fourth line shows the sequence number of the transposase encoded by the transfected mRNA. The column labeled "V%" in the fifth row shows the viability (percentage of living cells), and the column labeled "VCD" in the fifth row shows the total viable cell density (per ml millions of cells per cell) are shown. Rows 6-15 show these measurements at various time points after transfection, with the number of days since transfection indicated in column U.

Table 7. Transposition and excision activity of Orydias transposase variants Genes encoding Orydias transposase variants were designed, synthesized and cloned as described in Section 6.1.6.1. The sequence number for each variant is listed in column A. The gene was transformed into a Saccharomyces cerevisiae strain containing a single copy of the transposase reporter SEQ ID NO: 41 in its genome and plated on medium lacking leucine. After 48 hours, cells were scraped from the plates into minimal medium without leucine and with galactose as the carbon source. The A600 of each culture was adjusted to 2. The cells were cultured with galactose for 4 hours to induce transposase expression. The medium was diluted 1,000-fold with minimal medium lacking leucine. One 100 μl aliquot was then plated on agar plates in minimal medium lacking leucine and uracil (for measurement of transposon excision). Another 100 μl aliquot was plated on agar plates in minimal medium lacking leucine, tryptophan, and uracil (for measurement of transposon transfer). Each medium was also diluted 25,000 times and 100 μl aliquots were plated on agar plates in minimal medium lacking leucine (for live cell measurements). After 48 hours, count the colonies on each plate, with the number of colonies on the plate lacking leucine in column B, the number of colonies on the plate lacking leucine and uracil in column C, and the number of colonies on the plate lacking leucine, uracil, and tryptophan in column C. The number of colonies on the plate is shown in column D. Column E shows the resection frequency (calculated by dividing the number in column C by the number in column B, and then dividing by 25). Column F shows the metastasis frequency (calculated by dividing the number in column D by the number in column B, and then dividing by 25).

Table 8. Model weights of amino acid substitutions in Orydias transposase variants The effect of sequence changes on the excision and transposition activity of Orydias transposase was modeled as described in US Pat. No. 8,635,029. The mean and standard deviation of regression weights were calculated for each permutation. The position (relative to SEQ ID NO: 782) is shown in column A and the amino acid found at this position of SEQ ID NO: 782 is shown in column B. Amino acid substitutions tested are shown in column C. The regression weights of permutations regarding metastatic activity are shown in column D, the standard deviations of these regression weights are shown in column E, and the value obtained by subtracting the standard deviation from the average weight is shown in column F. The regression weights of permutations with respect to ablation activity are shown in column G, the standard deviation of this regression weight is shown in column H, and the average weight minus the standard deviation is shown in column I.

Table 9. Transposition and excision activity of Orydias transposase variants Genes encoding Orydias transposase variants were designed, synthesized, and cloned as described in Section 6.1.6.2. The sequence number of each variant is listed in column A. The gene was transformed into a Saccharomyces cerevisiae strain containing a single copy of the transposase reporter SEQ ID NO: 41 in its genome and plated on medium lacking leucine. After 48 hours, cells were scraped from the plates into minimal medium lacking leucine and containing galactose as the carbon source. The A600 of each culture was adjusted to 2. The cells were cultured with galactose for 4 hours to induce transposase expression. The medium was diluted 25,000-fold with minimal medium lacking leucine. Plate one 100 μl aliquot onto minimal medium agar plates lacking leucine and uracil (for measurement of transposon removal) and plate another 100 μl aliquot onto minimal medium agar plates lacking leucine, tryptophan and uracil. (for measurements of transposon transfer) and a third 100 μl aliquot was plated on agar plates in minimal medium lacking leucine (for measurements of live cells). After 48 hours, count the colonies on each plate, with the number of colonies on the plate lacking leucine in column B, the number of colonies on the plate lacking leucine and uracil in column C, and the number of colonies on the plate lacking leucine, uracil, and tryptophan in column C. Colony numbers are shown in column D. Column E shows the resection frequency (calculated by dividing the values in column C by the values in column B). Column F shows the metastasis frequency (calculated by dividing the value in column D by the value in column B).

7. REFERENCES All documents cited herein are specifically and individually indicated to be incorporated by reference in their entirety for all purposes. is incorporated herein by reference in its entirety to the same extent as if it were incorporated by reference. To the extent that information related to a citation may change over time, it means the version in effect on the effective filing date of the application, where the effective filing date is the date of the application in which the citation is first mentioned or of the priority application. means the filing date.

As will be appreciated by those skilled in the art, many modifications and variations of this invention can be made without departing from its spirit and scope. The specific embodiments described herein are provided by way of example only, and the invention is limited only by the terms of the claims appended hereto. is provided, along with the full scope of equivalents to which it is entitled. Unless clear from the context, any embodiment, aspect, element, feature, or step can be used in combination with any other.

Claims (38)

a transposon comprising a heterologous polynucleotide between left and right transposon ends, said left transposon end comprising SEQ ID NO: 7, and said right transposon end comprising SEQ ID NO: 8, wherein said transposon comprises SEQ ID NO: 8; A transposon capable of being transposed by a transposase having the sequence number 782. a sequence at least 90% identical to SEQ ID NO: 12 immediately adjacent to said left transposon end and between said left transposon end and said heterologous polynucleotide; and a sequence immediately adjacent to said right transposon end and between said right transposon end and said heterologous polynucleotide; 2. The transposon of claim 1, further comprising a sequence at least 90% identical to SEQ ID NO: 15 between the polynucleotides. 3. The transposon of claim 1 or 2, wherein the heterologous polynucleotide comprises a heterologous promoter active in eukaryotic cells. The heterologous promoter comprises i) an open reading frame, ii) a nucleic acid encoding a selectable marker, iii) a nucleic acid encoding a counter-selectable marker, iii) a nucleic acid encoding a regulatory protein, and iv) a nucleic acid encoding an inhibitory RNA. 4. The transposon of claim 3, wherein the transposon is operably linked to at least one or more of . 5. The transposon of claim 4, wherein the heterologous promoter comprises a sequence selected from SEQ ID NOs: 325-409. Transposon according to any one of claims 1 to 5, wherein the heterologous polynucleotide comprises a heterologous enhancer active in eukaryotic cells. 7. The transposon of claim 6, wherein the heterologous enhancer is selected from SEQ ID NOs: 304-324. Transposon according to any one of claims 1 to 7, wherein the heterologous polynucleotide comprises a heterologous intron capable of being spliced in eukaryotic cells. Transposon according to claim 8, wherein the nucleotide sequence of the heterologous intron is selected from SEQ ID NOs: 412-472. A transposon according to any one of claims 1 to 9, wherein the heterologous polynucleotide comprises an insulator sequence. A transposon according to claim 10, wherein the insulator sequence is selected from SEQ ID NOs: 286-292. The transposon of any one of claims 1 to 10, wherein the heterologous polynucleotide comprises or encodes a selectable marker. The selectable marker is selected from glutamine synthetase, dihydrofolate reductase, puromycin acetyltransferase enzyme, blasticidin acetyltransferase enzyme, hygromycin B phosphotransferase enzyme, aminoglycoside 3'-phosphotransferase enzyme, and fluorescent protein. The transposon according to item 12. the genome comprises a transposon comprising a heterologous polynucleotide between left and right transposon ends, said left transposon end comprising SEQ ID NO: 7, and said right transposon end comprising SEQ ID NO: 8, wherein said transposon A eukaryotic cell capable of being transposed by a transposase having the sequence SEQ ID NO: 782. 15. The cell of claim 14, wherein the eukaryotic cell is a mammalian cell. 16. The mammalian cell of claim 15, wherein the cell is a rodent cell or a human cell. 13. The transposon of any one of claims 1-12, wherein said heterologous polynucleotide comprises two open reading frames, each operably linked to a separate promoter. 18. The transposon of claim 17, wherein the heterologous polynucleotide further comprises a sequence selected from SEQ ID NOs: 596-779. Methods of integrating transposons into eukaryotic cells, excluding methods of integrating transposons in vivo,
a. A step of introducing into a cell a transposon comprising a heterologous polynucleotide located between left and right transposon ends, the left transposon end comprising SEQ ID NO: 7, and the right transposon end comprising SEQ ID NO: 8. process, and
b. introducing into the cell a transposase having a sequence at least 90% identical to SEQ ID NO: 782, wherein the transposase transposes a transposon to produce SEQ ID NO: 7 and SEQ ID NO: 8 sandwiching the heterologous polynucleotide; generating a genome comprising;
including methods. 20. The method of claim 19, wherein the transposase is introduced as a polynucleotide encoding a transposase. 21. The method of claim 20, wherein the polynucleotide encoding the transposase is an mRNA molecule. 21. The method of claim 20, wherein the polynucleotide encoding the transposase is a DNA molecule. 20. The method of claim 19, wherein the transposase is introduced as a protein. the heterologous polynucleotide encodes a selectable marker;
c. selecting cells containing the selectable marker;
24. The method according to any one of claims 19 to 23, comprising: A cell produced by the method according to any one of claims 19 to 24, wherein said cell is a mammalian cell. 26. The mammalian cell of claim 25, wherein the cell is a rodent cell or a human cell. A method of expressing a polypeptide comprising culturing a eukaryotic cell having a genome comprising a heterologous polynucleotide between left and right transposon ends, wherein said left transposon end comprises SEQ ID NO: 7. , and the right transposon end comprises SEQ ID NO: 8, and the heterologous polynucleotide is expressed. 28. The method of claim 27, further comprising purifying the polypeptide from the culture medium. 29. The method of claim 27 or 28, further comprising incorporating the purified polypeptide into a pharmaceutical composition. A polynucleotide comprising an open reading frame encoding a transposase having an amino acid sequence at least 90% identical to SEQ ID NO: 782, operably linked to a heterologous promoter. The transposase has E22D, A124C, Q131D, L138V, F149R, L156T, D160E, Y164F, I167L, A171T, R175K, K177N, T202R, I206L, I210L, N214D, V253I, V258L, I281F , A284L, L361I, V386I, M400L, S408E, L409I, F455Y, V458L, V467I, L468I, A514R, V515I, S524P, R548K, D549K, D550R and S551R. The polynucleotide according to paragraph 30. 31. The polynucleotide of claim 30, wherein the amino acid sequence of the transposase is selected from SEQ ID NO: 782 or 805-908. 33. A polynucleotide according to any one of claims 30 to 32, wherein said heterologous promoter is active in eukaryotic cells. 34. The polynucleotide of claim 33, wherein the eukaryotic cell is a mammalian cell. 35. The polynucleotide of claim 34, wherein the codons of the open reading frame are selected for expression in mammalian cells. An isolated mRNA encoding a transposase, wherein the amino acid sequence of the transposase is at least 90% identical to SEQ ID NO: 782, and the sequence of the mRNA is at corresponding positions between the mRNA and SEQ ID NO: 781. , an isolated mRNA comprising at least 10 synonymous codon differences to SEQ ID NO: 781. 37. The isolated mRNA of claim 36, wherein the codons of the mRNA at the corresponding positions are selected for expression in mammalian cells. A non-natural transposase encoded by a polynucleotide according to any one of claims 31 to 35 or an isolated mRNA according to claims 36 or 37 .